Note: Descriptions are shown in the official language in which they were submitted.
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TRANSFORMATION SYSTEMS FOR THE YEAST CANDIDA UTILIS AND
THE EXPRESSION OF HETEROLOGOUS GENES THEREWITH
BACKGROUND OF THE INVENTION
Field of the Invention
The present invention relates to reproducible
transformation systems of Candida utilis, more particularly
to the transformation of the yeast Candida utilis with
recombinant DNA, and to the expression of heterologous
genes in novel transformants obtained thereby. The present
invention also relates to novel DNA sequences which may be
used as selectable marker genes for transformation, and to
novel DNA sequences which may be used as promoters or
terminators for expressing heterologous genes. In
addition, the present invention relates to methods for the
efficient integration of heterologous genes into yeast
chromosomes.
Furthermore, the present invention relates to DNA
fragments having the properties of autonomous replication
as well as enhancing transformation efficiency in Candida
utilis, to methods for integrating DNA fragments having no
selectable marker gene into chromosome, and to methods for
obtaining DNA sequences having promoter activity.
Background Art
The development of gene manipulation technology has
made a.t possible to produce useful proteins in a large
amount with microorganisms. Prokaryotes such as Escherichia
coli or Bacillus subtilis can be used easily as a host
therefor, inter alia, E. coli being employed most
frequently as a host. However, proteins produced in E. coli
are often led to insoluble forms and cannot be glycosylated
upon secretion, so that these proteins are not satisfactory
for a variety of requisitions. In addition, pyrogenic
toxic factors produced by E. coli must be removed, when
proteins thus produced are intended to be used as
medicaments.
As compared with the use of these prokaryotic systems,
2I680~'~
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it is interesting to use eukaryotes such as yeast as a host
for producing useful proteins. First of all, yeasts of the
genus Saccharomyces or the yeast Candida utilis have been
known to be of a high safety, since Saccharomyces has been
long used for the production of fermentation products such
as alcoholic products and the yeast Candida utilis has been
used for the production of feeds. Moreover, yeast can be
generally cultured at a cell density higher than bacteria
as well as in a continuous mode. Yeast secretes proteins
into a medium, and the protein secreted is modified by
glycosylation. The production of proteins with yeast is
thus of worth when such modification is important for
biological activity of the protein.
Yeasts classified in the genus Saccharomyces have been
investigated most extensively, and genetic information of
them have been accumulated. The yeasts have been
investigated as a host for producing a variety of
substances. Further, transformation technology for some of
yeasts in addition to Saccharomyces such as those in
Pichia, Hansenula, Kluyveromyces, Candida genera has been
developed, and these yeasts are now examined as a host for
producing useful substances. Among them, the yeasts
assigned to the genus Candida, inter alia have properties
advantageous for practical use which are not found in the
yeasts of the Saccharomyces genus such as a wide anabolic
spectrum of the carbon source. The yeast of the genus
Candida is thus expected to be used for the production of
useful substances with recombinant DNA technology.
Among the yeasts of the genus Candida, Candida utilis
has an excellent anabolic ability to pentoses such as
xylose. In addition, Candida utilis, different from the
yeast of the genus Saccharomyces, does not produce ethanol
in culture under aerobic conditions and thus the growth is
not inhibited thereby. Therefore, it is possible to produce
cells efficiently by the continuous culture of Candida
utilis under a high cell density. Thus, attention has been
paid on Candida utilis as a protein source, and the
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industrial production of the yeast cell has once been
conducted with use of a saccharified liquor of broad-leaved
trees or a sulfite waste liquor containing a large amount
of pentoses. The yeast, Candida utilis, as well as
Saccharomyces cerevisiae and Saccharomyces fragilis has
been authorized by U.S. FDA (Food and Drug Administration)
as a yeast which can be used safely as a food additive.
Indeed, Candida utilis has been used even now as feeds in
many countries involving Germany, United States of America,
Taiwan and Brazil, and thus it can be said that the safety
of it has been confirmed.
In addition to the use of Candida utilis as a microbial
protein, it has been used widely in industry as a microbial
strain for fermenting pentoses or xylose or a microbial
strain for producing ethyl acetate, L-glutamine,
glutathione, invertase or the like.
However, any success has not been hitherto described or
proved in the transformation of the useful yeast, Candida
utilis. Failure in the transformation is believed due to
the extreme difficulty of obtaining mutant strains to which
a selectable marker such as an appropriate nutrient
requirement is introduced by mutagenesis treatment with a
conventional mutagen such as nitrosoguanidine or ethyl
methanesulfonic acid. This difficulty may be because of
the fact Candida utilis is a polyploid such as at least a
diploid. This can be also deduced from the fact that while
cloning of the genes such as ADEl and LEU2 of Candida
utilis, which have been frequently used in the other yeasts
as a selectable marker for transformation, have been
reported (Nishiya et al., Japanese Patent Laid-Open
Publication No. 66089/1992; Kobayashi et al., Japanese
Patent Publication No. 42673/1989), no Candida utilis host
strain having mutation in the corresponding gene has been
described. This means that it is almost impossible to
apply to Candida utilis a conventional technique for direct
selection of a transformant by introducing a complementary
gene for the nutritional requirement of a host strain which
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technique has been used for the development of a
transformation system in a variety of yeasts.
Moreover, Candida utilis has a high ploidy and no
sporulation ability, so that its genetic properties have
not been elucidated completely. Thus, the condition of
transformation as well as the condition to be satisfied by
a vector system remain unknown, so that it is expected
extremely difficult to establish the host/vector system.
Ho et al. discloses an examination of preliminary
transformation with a drug-resistant marker with respect to
Candida utilis (Ho, N. W. Y. et al., Biotechnology and
Bioengineering Symp., No. 14, 295 - 301, 1984). This
report is incomplete, since the condition of the
transformation experiment, or the exprimental data such as
Southern blot analysis of the drug resistant transformant
which is required for verification of the transformation
are not disclosed.
Therefore, it is still desired to establish a
reproducible transformation system with respect to Candida
utilis and a production technology of useful substances
with use of the system.
SUMMARY OF THE INVENTION
The present inventors have now obtained successfully
transformants from the yeast Candida utilis reproducibly,
and a variety of information on the expression of
heterologous genes in the transformant. The present
invention is based on these information.
An object of the present invention is thus to provide
a reproducible transformation system of Candida utilis.
Another object of the present invention is to provide
genes which are useful in the Candida utilis transformation
system as selectable markers, as target sequences at which
plasmid is integrated into chromosome, and as novel DNA
sequences such as promoter and terminator required for the
expression of heterologous genes.
A further object of the present invention is to provide
vector systems which make possible to express heterologous
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genes in Candida utilis.
Another object of the present invention is to provide
host/vector system into which the multiple copies of
heterologous genes can be stably integrated.
A further object of the present invention is to provide
process for expressing heterologous genes in Candida
utilis.
In addition, the object of the present invention is to
provide DNA fragments having an autonomous replicability
and a function for enhancing the transformation efficiency,
plasmid vectors containing the fragments, a process for
integrating a selectable marker gene-free DNA fragment into
chromosome with the plasmid vector, as well as a process
for obtaining DNA sequences having promoter activity and
novel DNA sequences having the promoter activity obtained
thereby.
The novel DNA sequences according to the present
invention includes a gene encoding the ribosomal protein
L41 of Candida utilis and its promoter and terminator
sequences; a cycloheximide resistance L41 gene; promoter
and terminator sequences of the phosphoglycerate kinase
(PGK) gene; promoter and terminator sequences of the
glyceraldehyde-3-phosphate-dehydrogenase (GAP) gene;
promoter and terminator sequences of the plasma membrane
proton ATPase (PMA) gene; the URA3 gene and its promoter
and terminator sequences; two DNA fragments having an
autonomous replicability; sequences having promoter
activity; and the ribosomal RNA genes encoding the rRNAs of
Candida utilis.
The vector which may be used in the transformation
system of Candida utilis according to the present invention
comprises a sequence homologous to the chromosomal DNA of
Candida utilis and a selectable marker gene, wherein a
heterologous gene is capable of being integrated into the
chromosomal DNA by homologous recombination, or comprises
a DNA sequence having an autonomous replicability in
Candida utilis and a selectable marker gene, wherein
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Candida utilis is transformed at high frequency.
In addition, the vector which may be used in the
transformation system of Candida utilis according to the
present invention comprises no selectable marker gene and
a sequence homologous to the chromosomal DNA of Candida
utilis, wherein a heterologous gene is capable of being
integrated into the chromosomal DNA by homologous
recombination. The plasmid can be used in transformation
together with a plasmid comprising a DNA sequence having an
autonomous replicability and a selectable marker gene.
Furthermore, the selectable marker gene which may be
used in the transformation system of Candida utilis
according to the present invention is a drug-resistant
marker which can function in Candida utilis, preferably the
L41 gene conferring cycloheximide resistance, a gene
conferring resistance to G-418, or a gene conferring
resistance to hygromycin B.
Furthermore, the process for expressing heterologous
genes in Candida utilis according to the present invention
comprises transforming Candida utilis with the vector
according to the present invention containing the
heterologous gene, culturing the transformant thus
obtained, isolating and purifying the expression product of
the heterologous gene from the culture.
In addition, the transformant of Candida utilis
according to the present invention refers to the one
obtained by the functional combination of the novel DNA
group, the vector systems and the like according to the
present invention.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 illustrates the restriction enzyme map, the
strategy for determining the DNA sequence of plasmids
containing the phosphoglycerate kinase (PGK) gene, and a
process for obtaining the promoter and terminator fragments
by PCR;
Figure 2 illustrates the DNA sequence of a DNA fragment
containing the PGK terminator;
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Figure 3 illustrates the DNA sequence of a DNA fragment
containing the PGK promoter;
Figure 4 illustrates a diagram for constructing
expression vector plasmids with the PGK gene promoter and
terminator;
Figure 5 illustrates the restriction enzyme maps of
plasmids containing the ribosomal DNA;
Figure 6 illustrates the structure of the ribosomal
DNA, the strategy for determining the DNA sequencing, and
the structure of subcioned plasmids, where Figure 6(a)
illustrates the structures of the plasmids pCREl, pCRE2,
pCRE3, pCRXl, pCRX2, pCRX3 and pCRX4, and Figure 6(b)
illustrates the restriction enzyme map of about 13; 5 kb DNA
fragment containing the ribosomal DNA of Candida utilis;
Figure 7 illustrates the restriction enzyme maps of
plasmids containing URA3 gene, and the complementation
ability for the Saccharomyces cerevisiae ura3-mutation of
these plasmids;
Figure 8 illustrates the strategy for determining the
DNA sequence of URA3 gene, and the restriction enzyme map
of it;
Figure 9 illustrates the DNA sequence of a DNA fragment
containing the URA3 gene;
Figure 10 illustrates the amino acid sequence deduced
from the DNA sequence of the URA3 gene, and the DNA
sequence of the DNA encoding it;
Figure 11 illustrates the continuation of Figure 10,
which are the amino acid sequence deduced from the DNA
sequence of the URA3 gene, and the DNA sequence of the DNA
encoding it;
Figure 12 illustrates the restriction enzyme maps of
plasmids containing L41 gene, and the strategy for
determining the DNA sequence;
Figure 13 illustrates the DNA sequence of a DNA
fragment containing L41 gene;
Figure 14 illustrates the amino acid sequence deduced
from the DNA sequence of the L41 gene, and the DNA sequence
21G803'~
_8_
of the DNA encoding it;
Figure 15 illustrates the construction of plasmids
pLCBSIO and pCLBSI2;
Figure 16 illustrates the construction of plasmids
pCLRE2, pCLRE3, pCLRXl and pCLRX2;
Figure 17 illustrates the results of examining the
viable cell ratio and the number of transformants of ATCC
9950 under a variety of electric pulse conditions;
Figure 18 illustrates the electrophoresis patterns of
the results of the Southern blot analysis of the DNA of the
ATCC 9950 strain transformed with plasmid pCLRE2;
Figure 19 illustrates the electrophoresis patterns of
the results of the Southern blot analysis of the DNA of
ATCC 9226, ATCC 9256 and ATCC9950 strains transformed with
plasmid pCLRE2;
Figure 20 illustrates the construction of plasmids
pCLRE4, pCLRES, pCLRE6 and pCLRE7;
Figure 21 illustrates the electrophoresis patterns of
the results of the Southern blot analysis of the DNA of
ATCC 9950 strains transformed with plasmids pCLRE4, pCLRES,
pCLRE6 and pCLRE7;
Figure 22 illustrates the electrophoresis patterns of
the results of the Southern blot analysis of the DNA of
ATCC 9950 strain transformed with plasmid pCLURAl;
Figure 23 illustrates the construction of plasmids
pCLSTAl and pCLRSTAl;
Figure 24 illustrates the result of the SDS
polyacrylamide gel electrophoresis of the supernatant of
the culture of the ATCC 9950 strain transformed with
plasmid pCLRSTAl;
Figure 25 illustrates the construction of plasmids
pCLLACl and pCLRLACl;
Figure 26 illustrates the construction of plasmids
pCLAPHl and pCLRAPHl;
Figure 27 illustrates the electrophoresis patterns of
the results of the Southern blot analysis of the DNA of
ATCC 9950 strain transformed with plasmid pCLRAPHl selected
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with different drug-resistant markers (CYHr:
cycloheximide-resistant; G418I: 6418-resistant);
Figure 28 illustrates the construction of plasmids
pCREB, pCRAPH2, pCRAPH3, pCRAPH4, pCRAPHS and pCRAPH6;
Figure 29 illustrates the restriction enzyme maps of
the plasmids containing glyceraldehyde-3-phosphate
dehydrogenase (GAP) gene, the strategy for determining the
DNA sequence, and the process for obtaining the promoter
and terminator fragments with PCR;
Figure 30 illustrates the DNA sequence of the DNA
fragment containing the GAP gene promoter;
Figure 31 illustrates the DNA sequence of the DNA
fragment containing the GAP gene terminator;
Figure 32 illustrates the construction of expression
vector plasmids with the GAP gene promoter and terminator;
Figure 33 illustrates the restriction enzyme map of the
plasmid containing the plasma membrane proton ATPase (PMA)
ger~e; the strategy for determining the DNA sequence, and
the process for obtaining the promoter and terminator
fragments with PCR;
Figure 34 illustrates the DNA sequence of a DNA
fragment containing the PMA gene promoter;
Figure 35 illustrates the DNA sequence of a DNA
fragment containing the PMA gene terminator;
Figure 36 illustrates the construction of expression
vector plasmids with the PMA gene promoter and terminator;
Figure 37 illustrates the structure of vector pGKAPH2
for cloning of DNA fragments containing ARS;
Figure 38 illustrates the restriction enzyme maps of
six plasmid insertion DNA fragments containing ARS;
Figure 39 illustrates the restriction enzyme maps of
insertion DNA fragments of plasmid pCARS6 and four plasmids
which contain subcloned DNA fragments of the plasmid
pCARS6;
Figure 40 illustrates the restriction enzyme maps of
insertion DNA fragments of plasmid pCARS7 and five plasmids
2I68Q37
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which contain subcloned DNA fragments of the plasmid
pCARS7;
Figure 41 illustrates the DNA sequence of an inserted
DNA fragment of the plasmid pCARS6-2;
Figure 42 is the continuation of the DNA sequences of
Figure 41, which illustrates the DNA sequence of an
inserted DNA fragment of the plasmid pCARS6-2;
Figure 43 illustrates the DNA sequence of an inserted
DNA fragment of the plasmid pCARS7-6;
Figure 44 is the continuation of the DNA sequences of
Figure 43, which illustrates the DNA sequence of an
inserted DNA fragment of the plasmid pCARS7-6;
Figure 45 illustrates the electrophoresis patterns of
the results of the Southern blot analysis of the DN.A ( 1 ) of
the ATCC 9950 strain transformed with plasmid pCARS6 or
pCARS7, and of the DNA (2) of the ATCC 9950 strain
transformed with plasmid pCLACl;
Figure 46 illustrates the electrophoresis pattern. of
the results of the Southern blot analysis of the DNA of
ATCC9950, ATCC9226, ATCC9256, KP-2059P and S288C strains
with CUARS1 (1) and CUARS2 {(2) and (3)} as probes;
Figure 47 illustrates the construction of promoter
cloning vector pPCV2;
Figure 48 illustrates the DNA sequence of a DNA
fragment having the promoter activity of plasmid pPCRVI9;
Figure 49 illustrates the construction of plasmid
pGKHPTl; and
Figure 50 illustrates the electrophoresis patterns of
the result of the PCR analysis of DNA of the ATCC 9950
strains transformed by the co-transformation method.
DETAILED DESCRIPTION OF THE INVENTION
Yeast Candida utilis
Specific strains of Candida utilis to which the
transformation system according to the present invention
can be applied include for example ATCC 9256 (IFO 0626),
ATCC 9226 (IFO 1086), ATCC 9950 (IFO 0988), IFO 0396, IFO
0619, IFO 0639, and KP-2059P.
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It has also been reported that electrophoresis pattern
of chromosomes varies among the strains of Candida utilis
and it shows the polymorphism in length of chromosomes
[Stoltenburg et al., Curr. Genet., 22, 441 - 446 (1992)].
It was expected that the transformation system according to
the present invention is limited in its application due to
its polymorphism. However, transformants were obtained and
the expression of heterologous genes were also confirmed
with either of the three strains employed in Examples
described below, while chromosomal polymorphism was
observed in the three strains. It would be anticipated for
a person skilled in the art that the transformation system
according to the present invention can be applied to
Candida utilis on the whole.
Transformation System
In order to develop a transformation system of
organisms, there are generally required three elements (,al
a selectable marker gene to select tran~formants, and a
method for selecting transformants, (b) an autonomously
replicable DNA sequence (ARS) required for the presence of
a plasmid DNA as an episome in a host cell, or the
homologous sequence of an appropriate chromosomal DNA
required for efficiently integrating a plasmid into a
chromosome (that is, the establishment of a target for
integrating the plasmid DNA), and (c) a method for making
a host cell capable of taking up an extranuclear DNA. All
of the three elements are required for obtaining
transformants. It was thus essential to examine and develop
all of these elements for establishing the transformation
system of Candida utilis where few genetic information have
been obtained.
(a) Selectable marker genes and selection of
transformants
When an auxotrophic mutant obtained by mutation
treatment can be used as a host, a gene which can
complement the auxotrophy can be used as a selectable
marker gene in order to select transformants. In this
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case, it is possible to select directly transformants in
the minimal medium which is free of the nutrient. However,
in the case of Candida utilis, it was impossible to develop
a transformation system using an auxotrophic complementary
gene as a selectable marker, since it was very difficult to
obtain a mutant strain to which an appropriate selective
mark such as an auxotrophy was added.
The present inventors have found that Candida utilis is
sensitive to drugs such as an antibiotic 6418, hygromycin
1U B or cycloheximide, and it is possible to suppress growth
by adding these drugs into the medium. The present
inventors have thus tried to use a gene which would confer
resistance to these drugs.
Thus, when a gene derived from the other organisms such
as the 6418 resistance gene (aminoglycoside
phosphotransferase gene) or the hygromycin B resistance
gene (hygromycin B phosphotransferase gene) is used, it is
preferred to use transcriptional promoter and terminator
sequences which function in Candida utilis to ensure the
expression of the gene.
In some of the yeasts in the Candida genus such as
Candida albicans, it has been described that some of the
codons are translated in a mode different from that in
other organisms (Ohama et al., Nucleic Acids Res., 21, 4039
- 4045, 1993). Thus, a heterologous gene used as a
selectable marker gene may not be always translated into a
protein having its function in the host. On the other hand,
there has been described the very interesting fact that the
sensitivity to cycloheximide is determined by an amino acid
residue at 56th position of the ribosomal protein L41
protein [Kawai et al., J. Bacteriol., 174, 254 - 262
(1992)].
The present inventors have thus obtained a gene of the
L41 protein of Candida utilis which is sensitive to
cycloheximide, converted the gene into the cycloheximide
resistance gene by the site specific mutation method, and
used it as a selectable marker gene. Since the gene was
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derived from the host, the gene was directly used with its
own promoter and terminator sequences for the expression.
Therefore, this embodiment is very advantageous in the
point that the gene can be surely anticipated for
expression.
Thus, the drug-resistance gene marker used as a
selectable marker in the transformation system of Candida
utilis according to the present invention is preferably a
cycloheximide resistance L41 gent. The DNA sequence of a
DNA fragment containing the L41 gene as well as the
promoter and terminator sequences is shown in Figure 13
(SEQ ID NO: 5), and the amino acid sequence deduced from
the DNA sequence is shown in Figure 14 (SEQ ID NO: 6). The
cycloheximide resistance L41 gene has a sequence shown in
Figure 13 where the 1644th nucleotide C has been converted
into A, and the 56th amino acid, Pro, in the sequence shown
in Figure 14 is converted into Gln.
In addition, another preferable drug resistance gene
marker which may be used in the transformation system
according to the present invention is the aminoglycoside
phosphotransferase (APT) gene which confers resistance to
the antibiotic 6418. As the aminoglycoside
phosphotransferase (APT) gene, two APT genes derived from
transposon Tn903 and transposon Tn5 have been known in the
art, and either of the two may be used in the present
invention. It is also possible to use the hygromycin B
phosphotransferase gene derived from E. coli which confers
resistance to the antibiotic hygromycin B in the
transformation system according to the present invention.
In the case of these heterologous genes such as 6418
resistance gene or hygromycin resistance gene,
transcriptional promoter and terminator which function in
Candida utilis for genetic expression are preferably
integrated at the 5'-upstream and the 3'-downstream of the
heterologous gene, respectively.
The promoter and terminator sequences for transcription
are preferably derived from the gene of Candida utilis. It
216 8 ~l ~'~
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is possible to use the promoter and terminator sequences of
the phosphoglycerate kinase (PGK) gene, the promoter and
terminator sequences of the glyceraldehyde-3-phosphate
dehydrogenase (GAP) gene, and the promoter and terminator
sequences of the plasma membrane proton ATPase (PMA) gene
in Candida utilis described hereafter. It is also possible
to use DNA sequences having promoter activity obtained with
a vector for the cloning of promoters described below.
In addition, the other promoter and terminator
sequences which can he used in the above described system
include promoter and terminator sequences of the genes in
Candida utilis homologous to the well-known genes such as
ADH, ENO, GAL and SUC in the yeast of the genus
Saccharomyces.
Furthermore, drug-resistance genes derived from
bacteria which may be used as selectable markers for
transformants include, in addition to tha above described
6418-resistance gene and a hygromycin P phosphotransferase
gene, antibiotic-resistance genes such as the
chloramphenicol acetyltransferase gene (chloramphenicol-
resistance) (Hadfield, C. et al., Gene, 45, 149-158
(1986)), the blasticidin deaminase (blasticidin-resistance)
(Izumi, M. et al., Exp. Cell Res., 197, 229 - 233 (1991)),
and the phleomycin-resistance gene (Wenzel, T.J. et al.,
Yeast, 8, 667 - 668 (1992)). In addition, well-known drug-
resistance genes such as the dihydrofolate reductase gene
(methotrexate-resistance) (Miyajima, A. et al., Mol. Cell
Biol., 4, 407 - 414 (1984)), the methyl sulfometuron-
resistance gene which is a dominant gene derived from yeast
(Casye, G.P. et al., J. Inst. Brew., 94, 93 - 97 (1988)),
the CUP1 gene (copper-resistance) (Henderson, R.C.A. et
al., Current Genet., 9, 133 - 138 (1985)), and the CYH2
gene (cycloheximide-resistance) (Delgado, M. et al., EBC
Congress, 23, 281 - 288 (1991)) may be used. When the
marker gene is derived from a heterologous organism such as
bacteria or transposon, it is preferred to use promoter and
terminator sequences which function in Candida utilis
- 15 -
described above.
(b) Establishment of targets for integration of
plasmid DNA
As described above, since applicable selectable markers
such as the cycloheximide-resistance L41 gene have been
established according to the present invention, it is
anticipated that a variety of sequences derived from
Candida utilis in addition to those sequences described
above can be used as target sequences.
According to the preferred embodiment of the prLsent
invention, it has been found that the gene encoding
ribosomal RNA (rDNA), the URA3 gene, the L41 gene, and the
PGK gene can he preferably used as appropriate chromosomal
DNA ~.r_agments required for integrating a plasmid into a
chromosome.
As for tine rRNA gene, it has been described that 100
copies or r:cre of rDNA are present in tandem on the
chromosome of Saccharomyces cerevisiae, and an autonomously
replicating sequence ( ARS ) is present in the repeating unit
(Saffer & Miller, JR. Molec. Cell. Biol., 6, 1148 - 1157
(1986)). It has been also described that the frequency of
integrative transformation can be increased by using the
rDNA region as the target for integration of a plasmid
(Lopes, et al., Gene, 79, 199 - 206 (1989)).
The present inventors have found that rDNA is present
repeatedly on the chromosome of Candida utilis. It has been
thus indicated that the rDNA of Candida utilis can be used
as a target sequence for integration in high frequency, and
indeed the rDNA was advantageously used as a recombination
target in the transformation system of Candida utilis.
It has been interestingly observed that when the yeast
of Candida utilis was transformed with the vector systems
according to the present invention described below which
target at chromosome of Candida utilis such as the rRNA
gene, the URA3 gene, the L41 gene or the PGK gene, a DNA
fragment was integrated into the chromosome and retained
stably in the yeast. It is thus possible to exclude the
2168037
- 16 -
problem of instability of a heterologous gene in the case
that a heterologous gene is retained as an extrachromosomal
plasmid which replicates autonomously.
It has been found as a result of the intensive analysis
of the mode of DNA fragments integrated in transformants
that the DNA fragments are integrated into the chromosome
of Candida utilis mainly by homologous recombination. This
means that a DNA molecule containing a DNA sequence which
has a homology to the chromosomal target sequence of a host
may be integrated into any chromosomal target.
Specifically, it is possible to integrate a DNA
fragment at any target sequence on the chromosome of
Candida utilis when the vector containing the DNA fragmen':
is digested at an appropriate restriction site in the Dr~A
sequence homologous to the target sequence to be a linear
plamrid i~w'A. In this case, when cycloheximide-resistance
I:~y gene is used as a selectable marker, transformants in
which a plurality of plasmid molecules have been integrated
at the same time are selected efficiently as described
below.
It is also possible to use a linear DNA fragment in the
form that a selectable marker is contained within a DNA
sequence having homology to a chromosomal target sequence.
In the transformation of this embodiment according to
the present invention, the DNA fragment is inserted to
chromosome and replace the homologous gene on chromosome.
Thus, no repetitive sequences of the target sequence is
thus formed at upstream and downstream of the DNA fragment
inserted. It is expected for the DNA integrated to have
higher stability.
In addition, the present invention has indicated that
the URA3 gene, the L41 gene, and the PGK gene which are
present in only two copies per cell as well as many other
genes can be used as targets for integrating a DNA
fragment. In general, yeast contains 100 copies or more
repetitive DNA unit containing rRNA genes of 18S, 5.8S, 25S
and 5S per haploid (Schweizer, E. et al., J. Mol. Biol.,
21603?
- 17 -
40, 261- 277 (1969)). Therefore, the use of the rDNA as a
target sequence of recombination is advantageous over the
use of the other gene sequences in the points that (1) the
frequency of transformation is expected to be increased,
and ( 2 ) the change in the target sequence by integration is
negligible. The present inventors have showed that the rRNA
genes are repetitively present in tandem in a repetitive
unit of about 13.5 kb DNA sequence also in Candida utilis
(described in de;:ails below), and that the transformation
frequency is increased 10 - about 50 times by using the
rDNA sequence as the target sequence of recombination as
compared to the case of the L41 gene having 2 copies per
cell as a target. It has been also she=~~n that DNA fragments
in the rDNA locus have high stability and ~~he rDNA sequence
is an excellent target for integration.
The use of the rDNA sequence as a target sequence for
integrating a DNA fragment in the present invention has
brought about the effect for increasing transformation
frequency and played an important role for the discovery of
a proper transformation condition among the treatment
conditions of yeast examined. However, it has been found
interestingly that the frequency of transformation is
decreased extensively when some of the rDNA regions are
used as targets of transformation. It has been indicated
that any of the rDNA fragments is not always used as a
target for efficiently integrating plasmids.
According to the further preferred embodiment of the
present invention, transformants having a plurality of
plasmids integrated therein can be obtained efficiently by
using cycloheximide-resistance L41 gene as a selectable
marker. The reason is considered as follows. Only when
plural copies of DNA fragments containing the
cycloheximide-resistance L41 genes are integrated, the
ratio of ribosome molecules in which the endogenous
cycloheximide sensitive L41 proteins are replaced by the
corresponding resistant proteins and are not inhibited in
functions by cycloheximide is increased. It is thus
.~
2~ 6~03'~
- 18 -
considered that the transformant can grow in the medium
containing cycloheximide. As the target site for
integration in this case, basically either of the sequences
can be used which is derived from the chromosome of Candida
utilis such as the URA3 gene locus, the L41 gene locus or
the like. It was also shown interestingly that the more
DNA fragments tend to be integrated by using the rRNA gene
locus inter alia as a target sequence for integration as
compared with the other gene loci as target sequences.
(c) Transformation method
As the method of transformation which makes a host cell
capable of easily taking up an extracellular DNA, the
conventional methods of the transformation of Saccharomyces
cerevisiae such ~~s the protoplast method, the lithium
acetate method, the electric pulse method, and
modifications thereof can be employed. While the
protoplast method is widFv_y used, it is rather complicated
in operation and often causes the problem of background
colonies as non-transformants in the selection of
transformants based on drug-resistance.
The present inventors have employed the lithium acetate
method and the electric pulse method to try the
transformation of Candida utilis with a plasmid as a
combination of the cycloheximide-resistance L41 gene and
the rDNA fragment described above, and found the conditions
in which transformants can be obtained reproducibly.
The transformation is preferably carried out by the
electric pulse method. Cells are grown up to a logarithmic
phase, and then washed and suspended into 1M sorbitol. The
condition of electric pulse includes the time constant
value (period of time for attenuating the voltage to about
37% of the maximum) of about 10 - 20 milliseconds, and the
viable cell ratio after the pulse of about 10 - 40%. For
instance, it has been shown according to the preferred
embodiment of the present invention that the above
described time constant value and the viable cell ratio
were obtained under the conditions of an electric
226~03'~
- 19 -
capacitance of 25 uF, a resistance of 600 - 1,000 S2, and a
voltage of 3.75 - 5 KV/cm, and about 500 - 1,400
transformants per 1 ug of DNA were obtained.
It has been also found that after electric pulse was
applied, a YPD medium containing 1 M sorbitol is preferably
added to the cell solution, and the mixture is shake
cultured. It has been also found that if the cells without
culture are directly spread on a selective plate containing
cycloheximide, no colony is obtained in some cases. The
culturing time is appropriately in t:~e r_anae of about .4 -
6 hours, and if the cells are cultured further, the growth
of the transformants cannot be negligible. Moreover, it is
preferred for the transformation according to the ;resent
irvention to enhance the transformation frequency by adding
a carrier DNA such as salmon sperm DNA on the contact of
the DNA and the cells or by adding polyethylene glycol.
The lithium acetate method (Ito et al., J. Bacteriol.,
153, 163 - 168, 1983) has been extensively used in txie
transformation of a yeast of the genus Saccharomyces
because of its simplicity and easiness. A variety of
modifications have been also described. We have confirmed
that Candida utilis may be transformed with these methods.
In particular, it is preferably to transform Candida utilis
with the modified lithium method in which ethanol is added
(Soni et al., Current Genet., 1993, 24, 455 - 459). It is
also possible to determine the optimal condition for the
transformation of Candida utilis by the lithium acetate
method and to enhance the transformation frequency by using
different conditions such as the cell densities on
collecting the cells, the lithium concentrations, the kinds
and concentrations of polyethylene glycol, and the kinds,
forms or amounts of a carrier DNA. These methods are
anticipated by a person skilled in the art, since (a)
selectable marker genes according to the present invention
and (b) targets for integration has been thus defined.
In addition, we have tried to carry out transformation
with plasmids containing a combination of eight ARS
2168~~?
- 20 -
sequences derived from Candida utilis which function in
Saccharomyces cerevisiae and a 6418-resistance gene
expressing unit which functions in Saccharomyces
cerevisiae, but no transformant was obtained. The
reproducibility of the transformation of Candida utilis
described by Ho et al (Ho, N.W.Y. et al., ditto) is thus
doubtful because of the result.
Expression vector systems and expression of heterologous
genes
According to the prese:~t invention, there provides
expression systems which can be used for the transformation
of Candida utilis.
An embodiment of the present inventio.r~ is a ri.asmid DNA
which comprises a sequence homologous to a chromosomal DNA
I5 of Candida utilis (referred to hereinafter as "homologous
DNA sequence" ) , which makes possible the integration of tile
pl3smi d DNA p_nto the chromosome by homologous rec~:ubination
at this portion, and a selectable marker for tine selection
of transformants.
The homologous DNA sequence preferably includes the
rRNA gene, the URA3 gene, the L41 gene, the PGK gene, the
GAP gene, and the PMA gene, which are preferably derived
from the chromosomal DNA of Candida utilis. It is possible
to integrate a heterologous gene into a desired position of
a chromosome depending on sequences used. The plasmid is
used in the linear form by the digestion at an appropriate
restriction site within the homologous DNA sequence of the
plasmid molecule. As a result, the plasmid DNA fragment is
integrated into the chromosome of Candida utilis by
homologous recombination.
In addition, according to the preferred embodiment of
the present invention, the DNA sequence containing a marker
gene and a heterologous gene is inserted at its both
terminals between the homologous DNA sequence within the
plasmid DNA. In this embodiment, the plasmid DNA is cut at
the homologous DNA sequence with restriction enzyme to
obtain a DNA fragment comprising a marker gene, a
~16863'~
- 21 -
heterologous gene, and the homologous DNA sequence at both
terminals of the fragment. The DNA fragment thus obtained
can be also integrated into the chromosomal DNA of Candida
utilis by homologous recombination.
The term "the DNA fragment thus obtained is integrated
into the chromosome of Candida utilis by homologous
recombination" herein, while its embodiment for integration
is not limited as far as the DNA fragment is integrated
into the chromosome of Candida utilis, refers to the
r~eanin~~ containing at least two embodiments as follows.
That is, the term refers to either of the meanings (1) an
embodiment being integrated into a chromosomal DNA by
causing homo~,ogous r c::ombination of the DNA sequence of the
chromosome wf Ca.ndida ut'lis and homologous DNA sequence
portions at the both terminals of the DNA fragment, which
is "inserted" into zhe cleaved portion; and (2) an
embodiment being .,.:~zegrated into a chromosomal DNA by
"replacing" a par ~ of the chromosome of Candicia utilis with
the plasmid DNA fragment by the homologous recombination of
the DNA sequence of the chromosome of Candida utilis and
the homologous DNA sequences provided at the both terminals
of the plasmid DNA fragment. In the embodiment of (2), the
DNA fragment integrated is anticipated to be present stably
in the chromosome, since the repetitive sequences of the
target sequence are not formed at the both terminals thus
inserted.
It is also preferred to use the above described drug-
resistance marker as the selectable marker gene, and more
preferred drug-resistance marker includes a gene conferring
resistance to cycloheximide such as the cycloheximide-
resistance L41 gene, the gene conferring resistance to an
antibiotic 6418 such as the APT gene derived from a
bacterial transposon Tn903, and the antibiotic hygromycin
B-resistance gene. When the selectable marker gene is
derived from microorganisms, it is preferred to ligate it
to a promoter which functions in Candida utilis to ensure
the expression.
~16~Q3'~
- 22 -
The vector according to another embodiment of the
present invention is a plasmid DNA which comprises a
sequence homologous to a chromosomal DNA of Candida utilis
(homologous DNA sequence), which makes possible the
integration of the plasmid DNA into the chromosome by the
homologous recombination at this portion, but no selectable
marker for the selection of transformants. The plasmid is
used in the linear form by digestion at an appropriate
restriction site within the homologous DNA sequence of the
1Q plas~uid molecule.
In the plasmid of this embodiment, the plasmid may be
constructed so that the DNA sequence containing a
he terologc?us gene is inserted at its both terminals between
t:z~ homologous DNA sequences. A DNA fragment having at its
both ~:erminals homologous DNA sequences is obtained by
cutting the plasmid DNA at the homologous DNA sequence with
restrict inn enzyme. The DNA fragment can also be integrated
ir.~o ;:he chromosomay DNA of Candida utilis by the
homologous recombination.
The DNA fragment in the linear form a.s integrated into
the chromosome of Candida utilis by homologous
recombination in the same manner as in the case of plasmid
DNA comprising a marker gene. It is also anticipated in the
plasmid of this embodiment that the DNA fragment integrated
is present stably in a chromosome by the integration
according to the embodiment (2) described above.
The homologous DNA sequence includes preferably the
rRNA gene, the URA3 gene, the L41 gene, the PGK gene, the
GAP gene, and the PMA gene. These genes are preferably
derived from the chromosomal DNA of Candida utilis. It is
also possible to integrate a foreign DNA fragment at a
desired position on a chromosome depending on the sequences
used.
The vector is used in transformation simultaneously
with a plasmid having a DNA sequence containing an
autonomously replicating sequence described below and a
selectable marker gene. It is possible to select
21~803'~
- 23 -
secondarily a strain that the selectable marker gene-free
DNA fragment has been integrated in the chromosome among
transformants which are selected by having the autonomously
replicable plasmid therein. The plasmid present in the
selected strain can be dropped out by culturing the cell
under a non-selective condition. As a result, a strain
which retains only the inserted DNA fragment on the
chromosome can be obtained. With this technique, it will
be possible to grow for example a strain which retains only
a heterologous gene awd is .free of extra sequences like a
drug-resistance gene derived from microorganisms.
Furthermore, a plasmid having a DNA sequence containing
the autonomously replicating sequence and- a selectable
marker gene can be used as a vector for the transformation
of the yeast Candida utilis. The plaamid tends to be
dropped by culturing the cell under a non-selective
condition, but a DNA fragment for enhancir:g stability can
be obtained as described below, so that fihe plasmid can be
used in combination with the DNA fragment as a vector.
The vector according to the present invention can be
linked to a heterologous gene to form a vector having the
heterologous gene retained therewith. By the
transformation of Candida utilis with the vector, the
heterologous gene can be integrated stably into the
chromosome of Candida utilis. The transformant thus
obtained can be cultured in an appropriate medium to give
the culture product, from which the expression product of
the heterologous gene is isolated and purified by the
method suitable for the expression product. That is, the
heterologous gene can be expressed Candida utilis. The
process for expressing a heterologous gene in Candida
utilis is provided. In this context, the term heterologous
gene generally refers to a gene or a DNA as a part thereof
which is not originally present on the chromosome of
Candida utilis as a host.
The heterologous gene is preferably combined with a
regulatory region which regulates independently the
216803'
- 24 -
expression of the heterologous gene or expressed under the
influence of the regulatory region of the gene disrupted by
the process of transformation. Such sequences should
function in Candida utilis, and include preferably for
example the promoter sequence and the terminator sequence
of the PGK gene, the GAP gene and the PMA gene according to
the present invention which is described below, and DNA
sequences riaving promoter activity obtained by a vector fox
cloning the promoter described below.
As apparent fro:~ ex,~mples described below, heterologous
genes such as the glucoamylase gene, the aminoglycoside
phosphotransferase.gene, the I3-galactosidase gene and the
hygromycin B phosphotrans~~erase g::ie have been successfully
expressed with the prom~~ter sequence and the terminator
sequence of the phosphoglycerate kinase gene according to
the present invention. An aminoglycoside phosphotransferase
gene has been also successful7.y expressed with the promoter
and terminator sequences o.f glyceraldehyde-3-phosphatE:
dehydrogenase gene as well as with the promoter and
terminator sequences of plasma membrane proton ATPase gene.
Among these heterologous proteins, glucoamylase is an
secreted protein, and aminoglycoside phosphotransferase and
~i-galactosidase are intracellular enzymes. This means that
a heterologous protein in either of an intracellular or
secreted protein can be produced in Candida utilis.
Furthermore, glucoamylase is also secreted and expressed at
a high level, and it can be said that Candida utilis is an
excellent host for the high production of a heterologous
protein.
Furthermore, it has been described that in some of the
yeasts of the genus Candida such as Candida maltose, or C.
albicans, a part of codons are translated in a mode
different from that in the other organisms (Ohama et al.,
Nucleic Acids Res., 21, 4039 - 4045 (1993)). This is
interpreted to be the reason why the expression product of
the ~-galactosidase gene derived from E. coli which has
been expressed in Candida maltose as a host exhibits no
2168437
- 25 -
activity. As apparent from the examples below, a (3-
galactosidase gene product derived from E. coli which has
been produced in Candida utilis retained its activity.
This shows that Candida utilis recognizes codons in normal
manner, and that Candida utilis is a preferred host in the
production of a heterologous polypeptide.
It is also possible to modify the properties of Candida
utilis by expressing a heterologous gene in Candida utilis.
Thus, according to the present invention, a process for
creating a novel Candida utilis strain is ~~ruvided . Fc~r
instance, it is possible to improve its fermentation
properties for increasing its industrial utility. In
part;_cular, a Candida utilis strain which is modified to
Axpress r: glucoamylase gene will have starch digesting
«bility, i.e., its carbon source spectrum is expanded.
Furtheriaoze, the vector according to the present
inv2:~tion can be used in the transformation of cells other
tian Candida utilis. When a cell other than Candida utilis
is used as a host, a DNA fragment suitable for the practice
of transformation is preferably selected. The DNA fragment
includes for example a bacterial plasmid DNA such as
pBluescript or pUCl9 in the case of E. coli. The DNA
fragment includes for example a yeast-E. coli shuttle
vector such as YEpl3 or YCp50 (Methods in Enzymology, 194,
p. 195 - 230, Academic Press (1991)) in the case of a yeast
of the genus Saccharomyces.
Method for cloning of DNA sequences having autonomous
replicability in the yeast Candida utilis
Furthermore, according to the present invention, a
method for cloning the DNA sequence having an autonomous
replicability in Candida utilis is provided. The DNA used,
which may be derived from any organisms, is preferably
derived from Candida utilis. As a vector for this method,
a vector containing a drug-resistance marker gene can be
used. Preferred examples include a vector containing the
APT gene which is a 6418-resistance gene and is expressed
by a promoter and a terminator functioning in Candida
21~8(l37
- 26 -
utilis. Specifically, a plasmid having the APT gene which
is expressed by the PGK gene promoter is used as a vector
to prepare a genomic DNA library of the Candida utilis
yeast, and Candida utilis is transformed with the library
DNA. Total DNA is extracted from a transformed yeast
selected on the basis of resistance to 6418. E. coli is
transformed with the DNA, so that the plasmid DNA present
in the transformed yeast as an extrachromosomal factor can
be recovered. Functional seq~~~.nces as aut~~nomous
replicating sequence (ARS) arp isol:~ted from the
chromosomal DNA fragment derived from Candida utilis
inserted in the plasmid DNA.
Surprisingly, when a plasmid contair;ing th=
cycloheximide-resistance L41 gene as a marker of res~.stance
to drug is used as a vector, any DNA sequance having an
nuLcnomous replicability could be cloned. In other wi~rds,-
even if the plasmid was used for preparing a Candida uti~_;;
yeast genomic Di~TA library and Candida utilis was
transformed with the library DNA, no cycloheximide-
resistant transformant was obtained. This indicates that
the ARS of Candida utilis has a feature-of producing a low
number copies per cell of the plasmid containing it, so
that a transformant cannot be selected even if it is
combined with the cycloheximide-resistance L41 gene which
requires several copies in order to select the
transformant. This has been further confirmed by the fact
that no transformant was obtained even by transforming
Candida utilis with a plasmid containing the ARS thus
obtained and the cycloheximide-resistance L41 gene. As
shown in examples below, it has been clarified by analyzing
extensively the properties of the DNA sequence containing
the ARS cloned that the plasmid containing ARS is present
in only about one copy per cell of the Candida utilis
yeast. In addition, the ARS thus cloned has also a feature
that the plasmid containing it is instable. When the
Candida utilis yeast was cultured for about 2.5 - 3.5
generations under a non-selective condition, the ratio of
2168x3?
- 27 -
the cells containing the plasmid was lowered to 20 - 30$
of the total number of cells.
Process for cloning DNA sequences having promoter activity
in Candida utilis
The process for cloning the DNA sequences having
transcriptional promoter activity in Candida utilis is
provided by using the DNA sequence having the above
autonomous repiicability. As the vector therefor, a vector
having... in addition to the DNA sequence having the
auton:.~;..ic:us reg~lic~bility, a drug-resistance gene free. of a
promoter sequence for transcription may be used. A vector
containing the APT gene which is a 6418-resistance gene can
be preferably used . D'vA . ..-.--.ad may be derived from any
organisms, prefera:~-iy derived from Candida utilis. In
addition, the DNA has to be converted to small molecules
for preparing a library by enzyme treatments with
restriction enzymes or DNl~~~e c?r by mechanir_aJ_ shear with
ultrasonic waves. A combination of twee restr_ction
enzymes of Alul, HaeIII and RsaI which recognize four
nucleotides in length and generate blunt ends is preferably
used for the partial degradation of the chromosomal DNA.
With this combination, more chromosomal regions are cloned
in the library.
More specifically, the Candida utilis yeast genomic DNA
library is prepared by the conventional method in which
about 0.8 - 1.8 kb DNA fragments which have been partially
digested with the above restriction enzymes are linked to
the 5' side of the promoter sequence-free APT gene.
Further, Candida utilis is transformed with the library
DNA. The yeast transformed with the plasmid in which the
DNA sequence having a promoter activity has been cloned
immediately before the APT gene becomes 6418 resistant.
Thus, the total DNA is extracted from the 6418-resistant
transformant to transform E. coli and the DNA sequence
having a promoter activity can be cloned efficiently . In
this case, promoter sequences having higher transcriptional
activities can be isolated by increasing the concentration
2I680~?'
- 28 -
of 6418 contained in the plate or selecting a strain which
forms a relatively large colonies on the plate. The method
according to the present invention is advantageous for
separating a promoter sequence having a high activity,
since the number of copies of the plasmid containing ARS in
Candida utilis remains about 1 per cell as described above.
Process for isolating the other functional genes of Candida
utilis
F~~=thern,ore, the process for isolating DNA having a
promoter. activity in Candida utilis according to tt~e:
present invention also provides a process for isolating DNA
sequences having a function for improving the stability of
the plasrr~id ont ~.ning ARS . An embodiment of the plasmid
containi:zn FRS in Can~:ida utilis is characterized in that
it has a lcw stability, and on culturing for 3 - 4
generations under a non-salective conditions the cells
retaining the = _asmi d are decr.Pa.sed to 20 - 30~ of the
total cells. T'tierefore, on the plate conta~.ning a selective
drug, a strain which retains ARS plasmid containing the
drug-resistance gene forms slightly smaller colonies as
compared with a strain that the drug-resistance gene has
been integrated on chromosome notwithstanding the number of
copies per cell being the same. In the present invention,
strains which form relatively large colonies were selected
for separating promoter sequences having high activity, so
that some of the separated DNA having promoter activity, as
described in Examples below, have functions which can
improve the stability of the plasmid. Moreover, it can be
anticipated for a person skilled in the art that the use of
this transformation system makes it possible to get DNA
sequences having a variety of functions such as a
centromere sequence.
Process for producing a transformant free from drug-
resistance marker gene
Another process for producing a transformant free from
drug-resistance marker gene is provided by using the above
DNA sequence having autonomous replicability according to
2I68Q3'~
- 29 -
the present invention. Specifically, a transformant free
from drug-resistance marker gene can be obtained by the
following procedure. First, a plasmid DNA having no
selectable marker gene for selecting the transformant and
containing a sequence homologous to the chromosomal DNA
(homologous DNA sequence) is digested at an appropriate
restriction enzyme site in this homologous DNA sequence
into a linear form. The lir~.ear plasmid DNA thus can be
integrated on the homologous Drlr sequnn~e- of the chromosome
of Candida utilis. The lineam.c~~.asmid DNF is used together
with a plasmid having DNA sequence containing an ARS and a
selectable marker gene for the transformation of yeast.
Among the transformants selected by the intrt~ductin~-. of the
plasmid containing ARS, clones in which ti:~ DNA fragme.rW
used for the transformation at the same time has been
integrated in the chromosome is secondarily selecr;ed by
trying the exrression of heterologous genes c~nt~i.ned in
the: DNA fragment or by confirming the integration of the
DNA fragment by PCR or Southern analysis. Furthermore, the
autonomously replicable plasmid present in the selected
strain can be easily removed by culturing the cells under
a non-selective condition. It is thus possible to obtain a
strain which is free of a selectable marker gene and
retains only the inserted DNA fragment on the chromosome.
Site-specific mutagenesis of chromosome of Candida utilis
According to another embodiment of the present
invention, a site-specific mutagenesis of chromosome of
Candida utilis is provided. In this method, a gene
fragmentation cassette in which a selectable marker gene
has been inserted into a target gene to lose its function
is used as a substituent of the chromosomal target gene.
The cassette has a linear DNA structure which comprises at
the both ends DNA sequences homologous to a chromosomal
target gene (homologous DNA sequence) and at least one
selectable marker gene between them. It is important that
the DNA fragment which can be inserted has the same
direction as it is on the chromosome. When yeast is
21680~'~
- 30 -
transformed with the cassette, the marker gene and the DNA
sequences which are present at its both sides and can be
inserted are integrated into the host. As a result of the
transformation, the target gene at the integration site is
disrupted and a yeast strain having a novel character is
obtained. The selectable marker gene is preferably a drug-
resistance gene, and the transformants of which the genes
have been disrupted can be selected by resistance to the
drug. The gene w'~lch car be a target of this gene
moc?~.fication is , ~?r~fAra~~ly ,a gene derived from the
chromosome of Candida utilis. Specifically, it includes
URA3, ADE1, ADE2, or HIS genes, ,bust it is not limited
thereto.
For instance, the Candida-~~util_is URA3 gene is split
with a selectable marker gene such as the cycloheximide-
resistance L41 gene to terminate its fuizction, and then
used for transformation. The cyc7.oneximide-resistant
transformant thus obtained has t~~~:~ URA3 genes cn the
chromosome, and one of the two genes has been disrupted.
Furthermore, a strain in which both of the URA3 genes have
been disrupted is obtained by transforming the strain, in
which one of the URA3 genes has been disrupted, with the
URA3 gene fragment split with the other selectable marker
gene such as a 6418-resistance gene. The ura3 variant is
known to become resistant to 5-fluoroorotic acid (5-FOA)
which is a toxic analogue of an intermediate in uracil
biosynthetic pathway. It is thus possible to obtain (as a
5-FOA resistant strain ) the ura3 mutant ( which has the URA3
genes both of which have lost the function ) by the gene
substitution of the strain in which one of the two URA3
genes has been disrupted. The ura3 mutant makes it
possible to obtain a transformant with the URA3 gene as a
selectable marker gene which is not a drug-resistance gene
marker. Furthermore, the auxotrophiic mutant thus obtained
has an advantage that it is scarcely influenced by the
secondary mutation which may be caused in the other gene
loci by the chemical mutation method.
2.~ 6803'
- 31 -
L41 gene
According to the present invention, the ribosomal
protein L41 of Candida utilis, a gene encoding it, its
promoter and terminator sequences are provided.
The protein L41 of Candida utilis according to the
present invention has an amino acid sequence described in
Figure 14 (SEQ ID N0: 6). Thus, the L41 gene according to
the present invention encodes the amino acid sequence
described in Figure 14. Moreover, a specific DNA sequence
comprising this gene, its promoter and terminator sequences
is shown in Figure 13 (SEQ ID NO: 5).
In addition, according to the present invention, a
cycloheximide-resistance L41 protein encoding mutant L41
gene in which the 56th amino acid residue has been
converted from proline to glutamine is provided. The
cycloheximide-resistance L41 gene can be used as described
above not only as a selectable marker gene for the
transformation of Candida utilis, but also as a selectable
marker gene for the transformation of the other yeasts such
as those of Saccharomyces genus. Furthermore, it is
needless to say that the promoter and terminator sequences
of the gene can be also used in the expression of
heterologous genes.
PGK gene
According to the present invention, the promoter and
terminator sequences of the PGK gene is provided.
Specific examples of the promoter sequence include
nucleotides 946 - 1346 of the DNA sequence shown in Figure
3 (SEQ ID NO: 2) and its partial sequences retaining the
promoter activity.
Specific examples of the terminator sequence preferably
include the DNA sequence shown in Figure 2 (SEQ ID N0: 1)
and its partial sequences retaining the terminator
activity.
An expression vector which may be used in Candida
utilis can be obtained by inserting the promoter and
terminator sequences into an appropriate plasmid vector.
2I68tt3'~
- 32 -
Examples of the plasmid vector include well-known E. coli
plasmids such as pBluescript and pUCl9 , and a yeast-E . coli
shuttle plasmid comprising a selectable marker gene such as
the cycloheximide-resistance L41 gene and, if necessary, a
DNA sequence homologous to a chromosomal target gene. It
would be anticipated for a person skilled in the art that
these sequences can be used as a promoter or terminator in
the other host cells, particularly a yeast of the genus
Saccharomyces.
The PGK gene is a gene encoding the enzyme in the
glycolytic pathway and is expressed in a large amount
together with the other genes encoding the enzymes of the
glycolytic pathway in Candida utilis. Thus, it is expected
to have a strong promoter. It is revealed in examples
described below that the promoter can be advantageously
used in the expression of a heterologous gene such as the
glucoamylase gene, the aminoglycoside phosphotransferase
gene or the a-galactosidase gene with use of the expression
vectors prepared.
In addition, it would be obvious for a person skilled
in the art that if the expression amount of a gene linked
to the PGK gene promoter and terminator sequences according
to the present invention is not decreased, the expression
vector can be miniaturized by defecting a part of these
sequences.
GAP gene
According to the present invention, the promoter and
terminator sequences of the GAP gene are provided.
Specific examples of the promoter sequence include
preferably the DNA sequence shown in Figure 30 (SEQ ID NO:
7 ) and its partial sequences thereof retaining the promoter
activity.
Specific examples of the terminator sequence include
preferably the DNA sequence shown in Figure 31 (SEQ ID NO:
8) and its partial sequences thereof retaining the
terminator activity.
An expression vector which can be used in Candida
Y
2~6~0~'~
- 33 -
utilis can be obtained by inserting the promoter and
terminator sequences to an appropriate plasmid vector.
Examples of the plasmid vector include well-known E, coli
plasmids such as pBluescript and pUCl9 , and a yeast-E . coli
shuttle plasmid comprising a selectable marker gene such as
a cycloheximide-resistance L41 gene and, if necessary, a
DNA sequence homologous to a chromosomal target gene can be
used. It would be anticipated for a person skilled in the
art that these sequences can be used as a promoter or
terminator in the other host cells, particularly a yeast of
Saccharomyces genus.
The GAP gene is a gene encoding the enzyme in the
glycolytic pathway and is expressed in a large amount
together with the other genes encoding the enzymes of the
glycolytic pathway in Candida utilis. Thus, it is expected
to have a strong promoter. It is revealed in examples
described below that the promoter can be advantageously
used in the expression of a heterologous gene such as the
aminoglycoside phosphotransferase gene with the expression
vector prepared.
In addition, it would be obvious for a person skilled
in the art that if the expression amount of a gene linked
to the GAP gene promoter and terminator sequences according
to the present invention is not decreased, the expression
vector can be miniaturized by defecting a part of these
sequences.
PMA gene
According to the present invention, the promoter and
terminator sequences of the PMA gene are provided.
Specific examples of the promoter sequence include
preferably the DNA sequence shown in Figure 34 (SEQ ID NO:
9) and partial sequences thereof retaining the promoter
activity.
Specific examples of the terminator sequence include
preferably the DNA sequence shown in Figure 35 (SEQ ID NO:
10) and partial sequences thereof retaining the terminator
activity.
21b8D37
- 34 -
An expression vector which can be used in Candida
utilis can be obtained by inserting the promoter and
terminator sequences to an appropriate plasmid vector.
Examples of the plasmid vector include well-known _E. coli
plasmids such as pHluescript*and pUCl9, or a yeast-_E. coli
shuttle plasmid comprising a selectable marker gene such as
a cycloheximide-resistance L41 gene and, if necessary, a
DNA sequence homologous to a chromosomal target gene can be
used. It would be anticipated for a person skilled in the
art that these sequences can be used as a promoter or
terminator in the other host cells, particularly a yeast of
Saccharomyces genus.
The GAP gene is a gene encoding the plasma membrane
enzyme, it is known in a Saccharomyces yeast to be a
primary protein comprising about 10% of plasma membrane
proteins. It is thus anticipated for the PMA gene to have
a strong promoter. It is revealed in examples described
below that the promoter can be advantageously used in the
expression of a heterologous gene such as an aminoglycoside
phosphotransferase gene with use of an expression vector
prepared.
In addition, it would be obvious for a person skilled
in the art that if the expression amount of a gene linked
to the PMA gene promoter and terminator sequences according
to the present invention is not decreased, the expression
vector can be miniaturized by defecting a part of these
sequences.
DNA sequences having promoter activities
According to the present invention, DNA sequences
having promoter ac,~ivities are provided. The DNA sequences
are isolated with use of a vector comprising an
autonomously replicable DIVA sequence and a drug-resistance
marker gene having no transcriptional promoter sequence.
Specific examples of the DNA sequence having the promoter
activity include preferably a DNA sequence shown in Figure
48 ( SEQ ID NO: 13 ) and a partial sequence thereof retaining
the promoter activity. In addition, as described in
* Trade-mark
64409-4
2168 3'~
- 35 -
examples below, eight DNA sequences were obtained in
addition to the DNA sequence of Figure 48 which has the
promoter activity. DNA sequences having promoter activities
can be also isolated by replacing the drug-resistance gene
having no transcriptional promoter sequence with the other
genes such as a hygromycin B-resistance gene. In addition,
it is also possible to obtain a promoter in which
transcriptional activity is induced under a specific
condition by changing the selection conditions such as
sugars contained in plate for selecting transformants or
the other medium composition. These would be easily
understood by a person skilled in the art by referring the
disclosure of the present specification.
An expression vector which can be used in Candida
utilis can be obtained by inserting the promoter and
terminator sequences to an appropriate plasmid vector.
Examples of the plasmid vector include well-known E. coli
plasmids such as pBluescript and pUCl9 , and a yeast-E . coli
shuttle plasmid comprising a selectable marker gene such as
the cycloheximide-resistance L41 gene and, if necessary, a
DNA sequence homologous to a chromosomal target gene can be
used. It would be anticipated for a person skilled in the
art that these sequences can be used as a promoter or
terminator in the other host cells, particularly a yeast of
Saccharomyces genus.
It is proved in examples described below that the
promoter can be advantageously used in the expression of a
heterologous gene such as an aminoglycoside
phosphotransferase gene with use of an expression vector
prepared.
In addition, it would be obvious for a person skilled
in the art that if the expression amount of a gene linked
to the promoter sequence according to the present invention
is not decreased, the expression vector can be miniaturized
by defecting a part of the sequence.
rRNA gene
According to the present invention, an about 13.5 kb
216~03'~
- 36 -
DNA fragment comprising the rRNA genes of Candida utilis
and a DNA sequence comprising the repetition of the
fragment are provided.
The about 13.5 kb fragment is represented by the
restriction enzyme map shown in Figure 6(b). The locations
of 18S, 5.85 and 25S rRNA genes in the DNA sequence are
shown in Figure 6(b).
The multiple-copies integration of a DNA fragment into
a chromosome is efficiently accomplished by using a partial
region of the rRNA genes as a target sequence. Plasmids
were constructed with four fragments which have been
obtained by dividing the about 13.5 kb DNA fragment into
four and used for transformation. It was interestingly
observed that the transformation frequencies thus obtained
were different depending on the regions used as the target
sequence for integration. While transformation frequency
was low in the plasmid pCLRES comprising a 2.4 kb EcoRI
fragment which comprises the 18S rRNA gene, transformants
were obtained in high frequencies in the plasmid pCLRE4
comprising a 3.5 kb EcoRI fragment which comprises a part
of the 3' side of 18S rRNA gene, the 5.85 rRNA gene and a
part of the 5' side of 25S rRNA gene, the plasmid pCLRE6
comprising a 3 kb EcoRI fragment which comprises a 25S rRNA
gene, and the plasmid pCLRE7 comprising a 4.7 kb EcoRI
fragment which comprises a part of the 5' side of 18S rRNA
gene.
URA3 gene
According to the present invention, the URA3 gene of
Candida utilis which is complementary to the ura3 mutation
of a Saccharomyces cerevisiae yeast is provided. The gene
can be used as described above as an integration target of
a DNA fragment and also used in the creation of a ura3
mutant by disrupting the chromosomal URA3 gene. The ura3
mutant as a host makes it possible to obtain a transformant
with the URA3 gene as a selectable marker gene which is not
a drug-resistance gene marker. In addition, it is obvious
that the promoter and terminator sequences of the gene can
21803'7
- 37 -
be also used for the expression of a heterologous gene.
The URA3 gene encodes the amino acid sequence shown in
Figures 10 and 11 (SEQ ID NO: 4). The URA3 gene includes a
gene comprising the DNA sequence shown in Figure 9 (SEQ ID
NO: 3 ) or having partial sequences thereof which retain the
function complementing the ura3 mutation of the
Saccharomyces cerevisiae yeast.
Autonomously replicating DNA sequence (ARS)
According to the present invention, autonomously
replicating DNA sequences which can retain the vector
containing the DNA sequence as episomal plasmids in Candida
utilis and enhance the transformation frequency of the host
are provided. The DNA fragment may be derived from any
organisms, preferably from Candida utilis. Specific
examples of ARS include preferably the DNA sequences shown
in Figures 41 and 42 (SEQ ID NO: 11) and in Figures 43 and
44 (SEQ ID NO: 12), and autonomously replicable partial
sequences thereof. Apparently from examples below, it is
also possible to transform the Candida utilis yeast with
the plasmids having shortened DNA fragments notwithstanding
the frequency being decreased.
A vector which can be present as a plasmid in Candida
utilis is provided by using ARS and an appropriate
selectable marker gene. Furthermore, DNA sequences having
promoter activities and DNA sequences having the other
functions are isolated by using the vector. It is also
possible to create a transformed yeast retaining only a DNA
fragment which contains no selectable marker gene but a
heterologous gene on a chromosome by using a plasmid
containing ARS and an appropriate marker gene and a plasmid
comprising a sequence homologous to the Candida utilis
chromosomal DNA (homologous DNA sequence) and having no
selectable marker gene for selecting transformants.
216803'
38
RXAMPT.F~
The present invention is further specifically
described with reference to the following examples, but it
is not limited to these examples.
In this disclosure, restriction enzyme sites in the
restriction enzyme maps of genes are represented by the
following.
Aa; AatII, Af; AfIII, Al; AfIIII, Ap; ApaI, B; BamHI, Bg;
BgIII,C; ClaI, E; EcoRI, RV; EcoRV, H; HindIII, Hp; HpaI,
K; KpnI, P; PstI, Pv; PvuII, S; SalI, Se; Spel, Sm; SmaI,
Sc; SacI, ScII; SacII, Sp; SphI, X; XbaI, and Xh; Xhol.
The methods used in the following examples are as
follows:
1) Deletion mutation treatment with ExoIII
nuclease and mung bean nuclease, and determination of DNA
sequence
After a plasmid (10 ug) was digested with a=
appropriate restriction enzyme, it was extracted ~~ith
phenol/chloroform and precipitated with ethanol to recover
DNA. DNA was dissolved in 100 u1 of an ExoIII buffer
solution (50 mM Tris-HC1, pH 8.0, 100 mM NaCl, 5 mM MgCl2,
10 mM 2-mercaptoethanol), 180 units of ExoIII nuclease, and
the mixture was incubated at 37cC. A 10 u1 portion of the
mixture was taken out at every one minute, and two portions
were combined and transferred to an ice-cooled tube in
which 20 u1 of an MB buffer (40 mM Na acetate, 100 mM NaCl,
2 mM ZnCl2, 10~ glycerol, pH 4.5) was placed. After five
tubes thus obtained were incubated at 65'C for 10 minutes
to inactivate the enzyme, five units of mung bean nuclease
was added, and the mixture was reacted at 37cC for 30
minutes. After the reaction, five DNA fragments having
different degrees of deletion was collected by agarose gel
electrophoresis. The DNA fragments thus collected were
treated with Klenow enzyme to form a blunt end and ligated
at l6cC overnight, and were used for the transformation of
E. coli.
3g 2168037
For insertion fragments of the plasmids thus
obtained, the sequencing reaction was carried out with a
fluorescent primer cycle sequence kit (Applied Hiosystems,
K.K.), and the DNA sequence was determined with an
automatic DNA sequences.
2) Hybridization
After agarose gel electrophoresis, DNA was alkali
transferred to a Hibond* N + filter ( Amersham ) according to
the protocol provided by the manufacturer to prepare a
filter for Southern hybridization.
The filter on which DNA was fixed was subjected to
prehybridization in a hybridization solution (6 x SSC, 5 x
Denhardt's Solution, 0.2% SDS, 20 ug/ml salmon sperm DNA)
at 65-C for 2 hours. A probe DNA labelled with Megaprime
DNA labelling systems and [a-~~P] dCTP ( 110 TBq/mmol ) was
added to the hybridization solution, and hybridization was
perfo-raed at 65~C for 16 hours. After hybridization, the
filter was washed in 1 x SSC containing 0.1% SDS at 65vC
for 2 hours and then sub j ected to autoradiography to detect
signals.
3) Composition of medium
The composition of a YPD medium for culturing yeast
contains 1% yeast extract, 2% bactopeptone and 2% glucose.
Agar was added in an amount of 2% to the medium in the case
_ of a plate form. The composition of a SD medium contains
0.67% yeast nitrogen base without amino acids and 2%
glucose. Amino acids were added to the medium depending on
the nutritional requirements of the yeast used. In the case
of a plate form, agar was added in an amount of 2% to the
medium. -
4) Treatment with enzyme
Treatments of DNA with enzymes such as a
restriction enzyme reaction, Klenow enzyme and T4 DNA
ligase were conducted under the conditions recommended by
the manufacturers or according to the methods described in
Molecular Cloning, 2nd edition, Sambrook et al., Cold
* Trade-mark
64409-4
2I6~03'~
Spring Harbor Laboratory Press (1989).
Example 1: Preparation of Candida utilis chromosomal DNA
The extraction of Candida utilis chromosomal DNA
5 was carried out by the following procedure. ATCC 9950
strain of Candida utilis was inoculated in 30 ml of YPD
medium and cultured at 30cC early stationary phase. The
cells were collected by centrifugation, washed with
sterilized water, and collected again by centrifugation.
10 After the cells were suspended in 3 ml of Zymolyase buffer
(0.9 M sorbitol, 0.1 M EDTA, 50 mM DTT, pH 7.5), 200 u1 of
0.9 M sorbitol containing 25 mg/ml Zymolyase 100T was
added, and the mixture was incubated at 37~C under shaking.
After the formation of protoplast was confirmed by
15 microscopic observation, the protoplasts were collected by
centrifugation. After 3 ml of lysis buffer ( 50 mM Tris-HC1,
mM EDTA, pH 8.0) was added and the protoplasts were
suspended gently and sufficiently in the buffer, 0.3 ml of
10% SDS was added, and the mixture was incubated at 65'C
20 overnight. Then, 1 ml of a 5 M potassium acetate solution
was added, and the mixture was left standing on ice for 1
hour. Precipitates were then removed by centrifugation, 4
ml of cold ethanol was added, and the mixture was
centrifuged to precipitate DNA. The precipitate was washed
25 with 50% ethanol, dried, dissolved in 3 ml of an RNase A
buffer ( 10 mM Tris-HC1, 1 mM EDTA, 50 ug/ml RNase A, pH
7.5), and incubated at 37cC for 30 minutes. Finally, 3 ml
of 2-propanol was added and the mixture was centrifuged to
remove the supernatant. Precipitates thus obtained were
30 washed with 50% 2-propanol and dried. The precipitate was
dissolved in 0.5 ml of a TE buffer and used as a Candida
utilis chromosomal DNA sample.
Example 2: Cloning of the phosphoglycerate kinase (PGK)
35 gene
After the partial digestion of the Candida utilis
chromosomal DNA with a restriction enzyme Sau3AI, the
2~68~37
41
digested mixture was layered on a 10 - 50$ sucrose density
gradient containing 0.8 M NaCl, 20 mM Tris-HCl, 10 mM EDTA
(pH 8.0), and centrifuged under 120,000 x g for 14 hours to
fractionate the DNA fragments. Among these fragments, 10 -
20 kb chromosomal DNA fragment was ligated overnight with
dephosphorylated ~.-phage vector DASHTMII (Stratagene
Cloning Systems) which had been digested with BamHI, and
then subjected to in vitro packaging to construct a Candida
utilis genomic DNA library.
The PGK gene of Candida util.i~ was cloned by the
hybridization using a known PGK gene of the other organism
as a probe. Specifically, filters on which about 20,000
plaques of the phage DNA of the above described DNA library
were adsorbed was prepared according to the method
described in Molecular Cloning, 2nd edition, Sambrook et
al., Cold Spring Harbor Laboratory Press (1989). Then, the
DNA fragment containing the PGK gene of Saccharomyces
cerevisiae was cut off as a 2 kb ClaI fragment from plasmid
pST2 which retains the PGK gene (Yamano et al., Journal of
Biotechnology, 32, 165 - 171 ( 1994 ) ) . The fragment was then
labelled with 32P and used as a probe for hybridization. As
a result, four positive plaques were cloned. The phage DNAs
prepared from each of these plaques were digested with a
variety of restriction enzymes and subjected to Southern
blot analysis using the same probe as the above. As a
result, a 2.6 kb EcoRI fragment and a 2.5 kb SalI fragment
hybridized with the probe were isolated.
Example 3: Determination of the DNA sequence of a
fragment containing the PGK gene, and characterization of
the structural gene and the regulatory regions
The 2.6 kb EcoRI fragment thus isolated was
inserted into the EcoRI site of a plasmid vector Bluescript
IISK+ to construct plasmids pPGKEl and pPGKE2 of which the
inserted fragments are opposite in their directions to the
vector. The 2.6 kb SalI fragment was also inserted into the
2~6$~~'~
42
SalI site of the vector Bluescript -IISK+ to prepare
plasmids pPGKSl and pPGKS2 of which the inserted fragments
are opposite in their directions to the vector (Figure 1).
From the plasmids pPGKEl and pPGKE2, plasmids
having various deletion mutations were obtained by
preparing deletion mutants at restriction enzyme sites such
as HindIII, Kpnl or Sall sites or by preparing a deletion
mutant with ExoIII nuclease and mung bean nuclease and the
DNA sequence of a 2530 by EcoRI fragment was determined.
The analysis of the region where the structural
gene was expected revealed a 1248 by open reading frame.
The homology to the PGK gene of Saccharomyces cerevisiae
was examined on the amino acid sequence deduced from the
DNA sequence of the open readir_g frame. These sequences
showed a homology of 86.8 to each other, so that the
isolated gene was concluded to be the PGK gene of Candida
utilis.
The EcoRI fragment contained 401 by fragment of the
upstream of the initiation codon ATG and 880 by fragment of
the downstream of the termination codon TAA as the
regulatory regions of the gene expression. The DNA sequence
of the 880 by fragment between the nucleotide next to the
termination codon TAA, and the EcoRI site which may contain
a transcription terminator is shown in Figure 2. Further,
from the plasmids pPGKSl and pPGKS2, plasmids having
deletion mutations were obtained by preparing deletion
mutants with ExoIII nuclease and mung bean nuclease in
order to determine the DNA sequence between the HindIII
site and the EcoRI site (Figure 1). The sequence of the
1346 by fragment between the HindIII site and the
nucleotide immediately before the initiation codon ATG
which may contain a transcription promoter is shown in
Figure 3.
Example 4: Construction of expression vectors with
the PGK gene promoter and terminator
In order to express a heterologous gene in Candida
r
21680~'~
43
utilis, a gene expression machinery which functions in
Candida utilis, that is, a transcription promoter and a
terminator are required. Expression vector plasmids having
a multicloning site was thus prepared between the PGK gene
promoter and the terminator of Candida utilis.
Firstly, fragments containing a promoter or a
terminator were prepared by Polymerise Chain Reaction
(PCR).
As the promoter, a fragment from the SalI site
located at the 2.3 kb upstream of the initiation codon to
. the nucleotide immediately before the initiation codon ATG
was prepared using the plasmid PGKS1 as a template. The
primers were Jynthesized with the following sequences in
which a Xbal site was created just before the initiation
codon at the 3'-end of the promoter fragment.
5'-GGTCGACATATCGTGGTAAGCGCCTTGTCA-3' (SEQ ID NO: 14)
5'-TTCTAGACTTTATCCGCCAGTATGTTAGTC-3' (SEQ ID NO: 15)
In addition, as the terminator, a fragment from the
nucleotide after the termination codon to the EcoRI site at
a 880 by downstream was prepared using the plasmid PGKEl as
a template. The primers were synthesized with following
sequences in which a KpnI site was created just after the
termination codon at the 5'-end of the terminator fragment.
5'-GGGTACCTAACTGCAAGCTACTTTGTAATTAAC-3' (SEQ ID N0:15)
5'-GGAATTCAACATGAATGACACGACGAAGGT-3' (SEQ ID N0:17)
The PCR process was conducted 30 cycles with Pfu
DNA polymerise (Stratagene Cloning Systems) and attached
buffer.
The promoter and terminator fragments synthesized
by the PCR process were digested with Sall and Xbal or with
KpnI and EcoRI, respectively. The fragments were
incorporated sequentially into the Sall - XbaI site and
Kpnl - EcoRI site in pUCl9 to construct a plasmid pPGKPT1
(Figure 4). After the EcoRI site at the 3'-end of the
terminator of the plasmid was treated with Klenow enzyme to
form a blunt end and ligated with NotI linkers (5'-
44
AGCGGCCGCT-3': SEQ ID NO: 18), the 0.9 kb PstI - NotI
fragment was prepared by digesting the plasmid with PstI.
The fragment and the 1.2 kb HindIII - PstI fragment cut out
from the plasmid pPGKSl was inserted between the HindIII
site and the NotI site of pBluescript SK- to construct a
plasmid pPGKPT2. Furthermore, pPGKPT2 was digested with
BglII, treated with Klenow enzyme and recyclized to remove
the BglII site in the terminator fragment and to construct
a plasmid pPGKPT3. After the HindIII site of pPGKPT3 was
then treated with Klenow enzyme to form blunt ends, the
fragment was ligated with Notl linkers (5'-AGCGGCCGCT-3':
SEQ ID NO: 18) to construct a plasmid pPGKPT4. The plasmid
nDGKPT4 was partially digested with KpnI, and the KpnI at
the upstream of the promoter was deleted to construct a
plasmid pPGKPT5 (Figure 4).
Example 5: Isolation of the rDNA
A 400 ng portion of 5 - 10 kb Sau3AI partially
digested DNA fragments of Candida utilis ATCC 9950 genomic
DNA obtained by the sucrose density gradient centrifugation
described in Example 2, and 200 ng of vector plasmid pBR322
digested with BamHI and dephosphorylated were ligated
overnight with T4 DNA ligase. E. coli DH5 was transformed
with this DNA solution to construct a Candida utilis
genomic DNA library.
Filters were prepared for about 10,000 colonies
according to the method described in Molecular Cloning, 2nd
edition, Sambrook et al., p. 12, 21 - 23, Cold Spring
Harbor Laboratory ( 1989 ) , and screened with the 1. 8 kb 3~P-
labelled HindIII - EcoRI fragment containing S. cerevisiae
18S rRNA gene as a probe. The rDNA fragment used as the
probe was prepared from a plasmid obtained from a genomic
DNA library of Saccharomyces cerevisiae S288C [a, suc2,
mal, gal2, CUP1] with a 32P-labelled oligomer corresponding
to the fragment of nucleotides 4 - 42 at 5'-terminal of
the 5.8S rRNA gene as a probe (Sone et al., Japanese Patent
2~6~~3'~
Publication No. 14865/1994).
Over 200 positive clones were obtained. Restriction
enzyme maps of plasmids from seven clones, pCRl, pCR4,
pCR5, pCR6, pCR7, pCR8 and pCR9 were constructed and
5 aligned for comparison. The restriction enzyme maps at the
both terminals were accorded (Figure 5). It has been found
from this fact that the region containing the rRNA gene of
Candida utilis has an about 13 kb repetitive structure.
From these plasmids, fragments cut out by digestion
10 with EcoRI or Xbal k~e~e subcloned into pBluescript SK- to
. construct plasmids pCREl, pCRE2, pCRE3, pCRXl, pCRX2, pCRX3
and pCRX4 (Figure 6(a)). Furthermore, these plasmids were
digested with a variety of restriction enzymes and
recyclized to construct a var.i.ety of deletion plasmids. DNA
15 sequences were determined on the insertion fragments of
these plasmids and the regions where the DNA sequence was
determined are shown by arrows in t'ie figure. The analysis
of the DNA sequences revealed the presence of the regions
which have high homology with the 185, 5.8S and 25S rRNA
20 genes. Thus, the location and transcriptional direction of
the three rRNA genes were determined (Figure 6(b)).
Example 6: Cloning of the orotidine 5'-phosphate
decarboxylase gene (URA3 gene)
25 A 100 ng portion of 5 - 10 kb Sau3AI partially
digested DNA fragments of Candida utilis ATCC 9950 genomic
DNA obtained by the sucrose density gradient centrifugation
described in Example 2, and 100 ng of vector plasmid YEpl3
(Methods in Enzymol., 194, 195 - 230, 1991) digested with
30 BamHI and dephosphorylated were ligated overnight with T4
DNA ligase. E. coli DH5 was transformed with this DNA
solution to construct a genomic DNA library. After the
plasmid mixture was extracted from the transformants,
Saccharomyces cerevisiae YPH 500 (ahis3, trpl, leu2, ade2,
35 lys2, ura3) (Stratagene Cloning Systems) which is a ura3-
strain was transformed with the plasmid DNA mixture and the
2168a3'~
46
transformants which did not require uracil for growth were
selected on a minimal medium. Transformation of S.
cerevisiae was conducted according to the lithium method
described in Methods in Yeast Genetics - A Laboratory
Course Manual - Rose M.D. et al., p. 122 - 123, Cold Spring
Harbor Laboratory Press, NY (1990).
Five Ura+ strains were obtained from 10 fag of DNA
by this procedure. Plasmid DNA was prepared from each of
these transformants according to the method described in
Methods in Yeast Genetics - A Laboratory Course Manual -
Rose M.D. et al., p. 130, Cold Spring Harbor Laboratory
Press, NY ( 1990 ) . E _ !,:oli was transformed with the DNA, and
a plasmid DNA was prep4red. Restriction enzyme maps were
constructed on 1;!~:e plasmids pCURA3-3 containing a 6.1 kb
insert and pCURA3-5 containing a 8.1 kb insert at the BamHI
site of YEpl3, respectively.
Example 7: Characterization of URA3 gene region
and determination of DNA sequence
In order to characterize the URA3 gene region, a 5
kb EcoRI fragment containing a region common to the
plasmids pCURA3-3 and pCURA3-5 was cut out from a plasmid
pCURA3-5 and ligated to the EcoRI site of a plasmid pRS314
(Stratagene Cloning Systems) to prepare a plasmid pURAEl
(Figure 7). The YPH 500 strain was transformed with the
plasmid by the lithium method. As a result, URA+
transformants were obtained in high frequency. This
indicates that URA3 gene is present in the 5 kb EcoRI
fragment, and one copy of the gene can complement the ura3
mutation of Saccharomyces cerevisiae.
Further, the plasmid pURAEl was digested with XhoI
or PstI and recyclized by the T4 ligase reaction to give
plasmids pURAEl~Xho and pURAEI~Pst.
Furthermore, the 3.5 kb EcoRI-ClaI fragment and the
2.3 kb HindIII fragment cut out from the plasmid pURAEl
were inserted between EcoRI and ClaI sites, or at the
2~6~03'~
47
HindIII site of the pRS314, respectively, to prepare
plasmids pURAECl and pURAHl (Figure 7).
The YPH500 strain was transformed with five
plasmids described above by the lithium method to examine
the complementarity of ura3- mutation and thus to examine
whether these fragments contain the URA3 gene or not. The
result is shown in Figure 7. The results showed that the
URA3 gene is located in 2.3 kb region between the EcoRI and
HindIII.
Further, the 2.3kb HindIII fragment containing the
. URA3 gene was ligated to the HindIII site of the plasmid
pBluescrip SK- to prepare a plasmid pURAH2. By the deletion
mutation with ExoIII nuclease and mung bean nuclease fro:;
both ends of the inserted fragment, plasmids having
deletion mutation were prepared, and the DNA sequence Taas
determined. The restriction enzyme map which has been
clarified by the DNA sequence and the sequence strategy ~:re
shown in Figure 8. The 2330 by DNA sequence thus obtained
is shown in Figure 9, and the deduced amino acid sequence
of the polypeptide consisting of 267 amino acid residues is
shown in Figures 10 and 11.
The amino acid sequence of the polypeptide was
compared with that of the URA3 protein of the other yeasts,
showing high homologies, for example 73.4% to Saccharomyces
cerevisiae, 76.3% to Kluyveromyces lactis, and 75.1% to
Candida albicans.
Example 8: Cloning of the L41 gene and
determination of the DNA sequence of a DNA fragment
containing the L41 gene
Filters were prepared for about 30,000 colonies of
the library prepared in Example 5 according to the method
described in Molecular Cloning, 2nd edition, Sambrook et
al., p. 12, 21 - 23, Cold Spring Harbor Laboratory (1989),
and screened with a 1.1 kb 32P-labelled Xbal - Sau3AI
fragment containing Candida maltosa L41 gene, RIM-C, as a
2~68D37
48
probe (Kawai et al., J. Bacteriol., 174, 254 - 262 (1992)).
Five positive clones were thus obtained.
Restriction enzyme maps of the three clones, pCL41-1,
pCL41-2 and pCL41-5 were constructed and compared with each
other. These clones have a 4 kb EcoRI fragment in common
(Figure 12). Southern hybridization analysis of these
plasmid DNA has revealed that a region which shows homology
to the L41 gene of Candida maltosa is present in the 1.4 kb
ClaI-Pstl fragment within the 4 kb EcoRI fragment.
The 4 kb EcoRI fragment was inserted into the EcoRI
site of pBluescript SK to prepare plasmids pCLEl and pCLE2
in which the fragment is inserted to an opp.c~~ite direction
with each other. From these two plasmi.ds, a variety of
plasmids having deletion mutations ~~ere obtained by
preparing deletion mutants with HindIII, XhoI or Clal
having a site within the EcoRI fragment or by preparing
u~letion :rutants with ExoIII nuclease and mung bean
nuclease in order to determine the 2086 by DNA sequence
from the BamHI site to the Sacl site (Figure 13).
Southern analysis revealed that a 318 by open
reading frame interrupted by a 367 by intron is present in
the region in which the presence of an L41 structural gene
is deduced (Figures 12 and 14). At the 5' and 3' terminals
and in the neighborhood of the 3' terminal in the region
which was deduced to be an intron, sequence GTATGT--
TACTAAC--AG which is common to intron was observed.
Further, the sequences were located at immediately after
the initiation codon as well as six L41 genes of the other
yeasts described by Kawai et al., J. Bacteriol., 174, 254-
262 (1992); Pozo et al., Eur. J. Biochem., 213, 849-857
(1993)). The deduced amino acid sequence of the Candida
utilis L41 polypeptide was compared with those of the L41
proteins of some other yeasts, showing high homologies, for
example 93.4% to Saccharomyces cerevisiae L41, 89.6% to
Candida tropicalis L41, and 85.8 to Candida maltosa L41.
2~.6~~137
49
Example 9: Preparation of cycloheximide-resistance
L41 gene by site-specific mutation
The amino acid at 56 position of the L41 protein of
a cycloheximide-resistant yeast is glutamine, while the
amino acid at the corresponding position in the L41 protein
of a cycloheximide-sensitive yeast is proline. It has been
reported that the sensitivity to cycloheximide of the yeast
is determined by this amino acid residue of the L41 protein
~Kawai et al.,~ J. Bacteriol., 174, 254-262 (1992)). In
~ddit~~~n, the amino acid at 56 of the L41 protein of a
cycloheximide-sensitive Candida utilis was proline like
that of a cycloheximide-sensitive Saccharomyces cerevisiae.
The codon encoding :'she proline at the 56 position of the
L41 gene w~changed ir~to a glutamine codon by site-
specific mutagenesis in order to convert the L41 protein
encoded by the gene info a cycioheximide-resistant protein,
which was used as a selectable marker of transformation.
Firstly, a 2.1 kb BamHI-SacI fragment obtained from
the plasmid pCLEl was inserted between the BamHI and SacI
sites of pUCl8 to prepare a plasmid pCLBSl (Figure 15).
Further, 0.6 kb fragment obtained by digesting the
plasmid pCLEl with AflII, treating with Klenow enzyme to
form blunt ends and further digesting with Xhol was
inserted between the SmaI and Xhol sites of pBluescript SK-
to prepare pCLAXl. In this plasmid, the AflII site is
regenerated by the ligation of the blunt AflII end of the
0.6 kb fragment and the SmaI end of a vector. A single
stranded DNA was prepared from pCLXAl with a helper phage,
and a mutant plasmid was prepared with a synthetic
oligonucleotide 5'-TTG TGG AAA ACT TGC TTG GTT TGA-3' and
a Sculptor In Vitro Mutagenesis Kit (Amersham). DNA
sequence of the 0.6 kb insertion fragment on the candidate
plasmid thus obtained was determined, and a plasmid pCLAX20
in which no mutation in the DNA sequence was found except
that the 56th proline codon CCA had been mutated into a
glutamine codon CAA was obtained.
21fi~~3'~
A 0.6 kb insertion fragment was cut out as a Clal
AflII fragment from pCLAX20 and ligated with a 4.4 kb
fragment obtained by digesting the plasmid pCLHSl with Clal
and AflII to construct a plasmid pCLBSIO containing a
5 mutated L41 gene.
The plasmid pCLBSIO was digested with BamHI and
Sphl, treated with T4 DNA polymerase to form blunt ends,
and NotI linkers (5'-AGCGGCCGCT-3') were inserted to
prepare a plasmid pCLBSI2 (Figure 15).
10 It was examined whether the mutated L41 gPre thus
obtained confers yeast resistance to cycloheximide or not.
A 2.1 kb BamHI-SacI fragment containing the mutated L41 ,
gene why.~_h was obtained from the plasmid pCLBSIO was
__r.serted between the BamHI and SacI sites of YEpl3K a YEp
15 vector (Sone et al., Appl. Environ. Microbiol., 54, 38-42
(1988)) to prepare a plasmid pYECLIO. On the other hand, a
2.1 kb :~smHI-SacI fragment containing the wild type L41
gene obtained from pCLHSl was cloned into the YEpl3K to
prepare a plasmid pYECLI as a control.
20 A Saccharomyces yeast strain YPH 500 was
transformed with these plasmids according to the lithium
acetate method described in Methods in Yeast Genetics - A
Laboratory Course Manual - Rose M.D. et al., p. 122 - 123,
Cold Spring Harbor Laboratory Press, NY (1990). Leucine
25 non-requirement strains were selected as transformants.
These transformants were grown on YPD plate containing
cycloheximide. As a result, the strain retaining pYECLIO
grew on the YPD plate containing cycloheximide. On the
contrary, the strain retaining pYECLl did not grow on the
30 YDP plate containing cycloheximide. It was thus proved that
the mutated L41 gene thus prepared conferred resistance to
the cycloheximide-sensitive yeast.
Example 10: Construction of plasmids for
35 transformation and determination of the conditions of
transformation in Candida utilis
Firstly, transformation of Candida utilis ATCC 9950
216~Q3'~
51
strain was tried with plasmids containing the expression
cassette of a 6418-resistance gene (aminoglycoside
phosphotransferase (APT) gene) which had been proved to
function in Saccharomyces cerevisiae. The expression
cassette was prepared by ligating a 1.1 kb 6418-resistance
gene which was cut out as a Xhol-PstI fragment from a
plasmid pUC4K ( Pharmacia ) and converted into the one having
blunt ends between the 1.0 kb promoter region of the
glyceraldehyde-3-phosphate dehvdrogenase gene and the 0.4
kb terminator region of the phosphoglycerate kinase gene
described by Yamano et al., J. Biotechnol., 32, 165-171
(1994). Some plasmids were used, i.e.. (1) a plasmid in
which the above cassette was ligated to vF:pl3 K as a YEp
vector; (2) A DNA library in v:hich San3AI partially
digested chromosomal DNA fragments (5 - 10 kb) of the
Candida utilis ATCC 9950 strain describea in Example 2 were
inserted into the BamHI site of a plasmid pGPDAPHI which
was constructed by the above expression cassette was
ligated to plasmid pBluescript SK-, and (3) eight plasmids
of pGPDAPHl containing ARS sequences which function in
Saccharomyces cerevisiae. The plasmids in (3) were isolated
from yeast colonies which were obtained by transformation
of Saccharomyces cerevisiae YPH 500 strain with the library
in (2). The transformation of Candida utilis ATCC 9950
strain was carried out with these plasmids or library DNA
by the electric pulse method with various combinations of
resistance and voltage or the lithium acetate method.
However, no colonies exhibiting resistance to 6418 were
obtained.
As the next stage, four rDNA fragments cut out from
the plasmids pCRE2, pCRE3, pCRXl and pCRX2 described in
Example 5 (Figure 6) with EcoRI or Xbal were inserted into
the EcoRI site or the Xbal site in the plasmid pCLBSIO
described in Example 9 (Figure 15) to construct plasmids
pCLRE2, pCLRE3, pCLRXl and pCLRX2.
Transformations of Candida utilis ATCC 9950 strain
216~~37
52
were carried out by the electric pulse method with various
combinations of resistance and voltage and the lithium
acetate method with four plasmids having a cycloheximide-
resistance gene as a selectable marker, and a library DNA
which was prepared by inserting the Sau3AI partially
digested DNA fragments (5 - 10 kb) of the chromosomal DNA
of Candida utilis ATCC 9950 strain into the BamHI site in
the plasmid pCLBSIO. However, when these plasmids were used
in the cycl~.c~ form, no Iransformants were obtained. During
this tran:;fo.rmation experiment, the appearance of pseudo-
resistant colonies which exhibited low resistance to
cycloheximide or resistance to 6418 was observed. The
pseudo-resistant colonies refer to those which are often
observed in the select;. an of transf~rmants on the plate
having antibiotics such as 6418 or cycloheximide added
thereto and spontaneously acquire resistance regardless of
the presence of the drug-resistance gene of a selectable
marker.
In this experiment, when cycloheximide was used for
the selection of transformants, it was revealed that the
appearance of pseudo-resistant colonies was suppressed by
setting the concentration of cycloheximide in the plate at
40 pg/ml and incubating the plate at a temperature of 28'C
but not 30'C. Thus, the transformation experiments were
conducted with the plasmids pCLRE2, pCLRXl and pCLRX2 which
had been digested with BglII, EcoRV and BglII,
respectively, at the restriction enzyme sites within the
rDNA region of the plasmid DNA in order to promote the
integration of the DNA into the chromosome. As a result,
cycloheximide-resistant clones were successfully obtained
with use of the BglII digested plasmids pCLRE2 and pCLRX2
under the condition of electric capacitance of 25 uF,
resistance of 600 S2 and voltage of 5 KV/cm. These resistant
strains have sizes obviously larger than those of a small
pseudo-resistant strains obtained only seldom in a control
experiment that no plasmid DNA was added, and were provided
to be the transformants from the result of Southern
2168~3'~
53
analysis shown in Example 12.
In order to find the optimal condition of
transformation, electric pulse experiments were conducted
with the BglII digested plasmid pCLRE2 under conditions at
a fixed electric capacitance at 25 uF with various
combinations of resistance and voltage. The results are
shown in Figure 17, in which the post-pulse viable cell
ratio and the number of cycloheximide-resistant
transformants thus obtained are shown.
It has been found from the results that
transformants are obtained in a high frequency of about 500
- 1, 400 cells per 1 ug DNA under the conditions of electric
can=citance of 25 pF, resistance of 600, 800 or 1,000 S
and voltage of 3.75 or 5 KV/cm. The post-pulse viable cel:~..
ratio was about 10 - 40 % under these conditions . The viable
cell ratio was 40 % or less in some conditions of resistance
of ~u0 or 400 S2, but high frequencies of transformation
were not obtained. At the resistance of 200 or 400 S~, time
constant (time required for the attenuation of voltage to
about 37% of the maximum) was in the range of 10
milliseconds or less. Further, under the conditions of the
resistance of 600, 800 or 1, 000 S2 and the post-pulse viable
cell ratio of about 10 - 40%, time constant was in the
range of about 10 -20 milliseconds. These results suggested
that it is important for obtaining a high transformation
frequency to apply the electric pulse to cells so that the
post-pulse viable cell ratio is in the range of about 10 -
40% and the time constant is in the range of 10
milliseconds or more.
Moreover, it is preferred to add YPD medium
containing 1 M sorbitol to the cell solution and culture it
with shaking after the electric pulse was applied. If the
cells were directly spread on the selective plate
containing cycloheximide without culture, no colonies were
obtained.
In addition, the variations of the number of viable
cells and the number of transformants were examined with
.~.. 216803rd
54
the passage of time, and their rates of increase were
compared to determine the optimal culturing time.
As a result, it was found that the rate of increase
of transformants was higher than that of the number of
viable cells during 6 hours of culture, but the number of
viable cells and the number of transformants increase at
the same ratio after 6 hours of culture. It was thus
revealed that culture time of 6 hours was optimal.
The standard method for transformat~.nn of Candida
utilis ATCC 9950 strain by electr~.c pulse is described in
Example 11.
Example 11: Method for transformation of Cam~?i:~a
utilis ATCC 9950 strain by electric pulse
After the colony grown on YPD plate is cultured
with shaking in 5 ml of YPD liquid medium at 30~C for about
8 hours, ~ t is inoculated in 200 ml of YPD liquid mediu5 ; wat
a concentration of-. 0D600 = 0 ~ 0024 and cultured with ~:haking
at 30~C for about 16 hours. After the cells have grown to
logarithmic growth phase (0D600 - 2~5), cells are collected
by centrifugation at 1, 400 x g for 5 minutes. The cells are
washed once with 100 ml of ice-cooled sterilized water,
once with 40 ml of ice-cooled sterilized water, and once
with 40 ml of ice-cooled 1 M sorbitol. After the cells are
suspended into 10 ml of 1 M sorbitol, they are transferred
in sterilized polypropylene tube and centrifuged again at
1,100 x g for 5 minutes. After the supernatant is removed,
the cells are suspended in an ice-cooled 1 M sorbitol so as
the volume of the final cell solution to be 2.5 ml.
The experiment of transformation by electric pulse
is carried out with a Gene Pulser (Bio-rad). After 50 u1 of
the cell solution is mixed with 5 u1 of a DNA sample, the
mixture is placed in a 0.2 cm disposable cuvette, and
electric pulse is applied under an appropriate condition.
After the application of pulse, 1 ml of ice-cooled YPD
medium containing 1 M sorbitol is added, and the mixture is
21~8~~7
transferred in a sterilized polypropylene tube and
cultured with shaking at 30'C for about 6 hours. After the
culture, the cell mixture was spread on the YPD selectable
medium containing 40 ug/ml of cycloheximide and mairitained
5 at 28'C for 3 or 4 days to obtain the colonies of the
transformants.
Example 12: Detection of the plasmid DNA in the
transformant~ by Southern analysis
10 Sever. strains among the cycloheximide-resistant
colonies obtained in Example 10 were analyzed by the
Southern blot techniauP to examine whether these clones
retained the plas~~id DNA ~r not. Chromosomal DNA was
prepared according ~o the methc3 described in Methods in
15 Yeast Genetics - A Laboratory Course Manual - Rose M.D. et
al., p. 131-132, Cold Spring i~arbor Laboratory Press, NY.
The DNA thus prepared was ;iigested with FcoRV or S~1_I and
hybridized with a i.~3 kb 32P-labelled BamHI-HindIII
fragment containing the L41 gene (Figure 12) as a probe
20 (Figure 18).
As a result, in addition to the 5 kb band derived
from the endogenous L41 gene, the band over 20 kb was
detected by digestion with EcoRV. EcoRV cuts the rDNA locus
but not the plasmid pCLRE2. It was thus considered that the
25 detection of the over 20 kb band was due to the integration
of the plasmid into the chromosome. Southern analysis in
Example 15 proved that there are 2 copies of the L41 gene
in one cell of Candida utilis. In consideration of the
result of densitometric analysis, it was revealed that the
30 number of copies of integrated plasmid DNA was in the range
from about 6 copies (lane 7) to 15 copies (lane 2).
On the other hand, SalI cuts the plasmid pCLRE2 at
one position. 4Jhen the chromosomal DNA was digested with
SalI, a 8.5 kb band corresponding to the length of the
35 plasmid pCLRE2 was detected in addition to the 7.5 kb band
derived from the endogenous L41 gene. The 8.5 kb band was
~16~037
56
considered to be generated by Sall digestion of vicinal
plasmids due to tandem integration of plural plasmids in
the chromosome.
In addition, when Southern analysis was conducted
on 10 or more cycloheximide-resistant strains, the presence
of the plasmid DNA was confirmed in all of the clones. The
cycloheximide-resistant strains obtained in the
transformation experiments in Example 10 were proved to be
the transformants.
1_7
Example 13: Transformation of the other Candida
utilis strains
It hay been reported that Candida utilis has
differE~nt chromosoma_'._ electrophoresis patterns depending on
strains and exhibits the polymorphism of chromosomal length
(Stoltenburg ez al., Curr. Genet., 22, 441-446 (1992).
Because of t~~c: anticipation of difference in genetic
properties or transformation frequency depending on
strains, transformation by the electric pulse method
described in Example 11 was examined also on ATCC 9226 and
ATCC 9256 strains in addition to the ATCC 9950 strain.
Pulse was applied under the condition of electric
capacitance of 25 uF, resistance of 1,000 S2 and voltage of
2.5 - 6.25 KV/cm. As the plasmid DNA, 2 ug of pCLRE2
digested with BglII was used.
The result are shown in Table 1. While the
frequency was different depending on strains,
cycloheximide-resistant colonies were obtained in any of
the strains.
2~6803'~
57
Table 1: Transformation with plasmid pCLRE2
Voltage Condition Number of transformants
per 2 ug of DNA
(KV/cm) ATCC 9226 ATCC 9256
2.50 22 0
3.75 145 8
5.00 128 18
6.2.5 94 7
With Tespect to e~g:~t ~y ;-?_o:~ex. i mide-resistant
' strains in total, i.e., four strains derived from ATCC 9226
and four strains derived from ATCC 9256 a,~ '-ell as two
cycloheximide-resistant strains derived from AT~;: 9950 as
controls, chromosomal DNAs were prepared a-d uigested with
BglII. Southern analysis of the DNA was cond~:~cted with a
3ZP-labelled 1.8 kb BamHT-HindIIT rragment containing the
Lr.i gene (Figure 12) as a probe.
The r.es-u.lts are shown in Figure 19. A o:::rd cer~.ved
from the plasmid DNA was observed in addition to the 5.4 kb
band derived from the endogenous L41 gene on the chromosome
in either of the strains. This indicates that these
resistant strains are transformants retaining the plasmid
DNA.
In some of the transformants derived from ATCC 9226
and ATCC 9256 strains, bands were observed in higher
molecular weight in addition to the 8.4 kb band having the
same size as plasmid DNA (lanes 2 - 4 and 7). This
indicates that when the rDNA sequence on the plasmid is not
identical to the rDNA sequence on the chromosome as the
integration target, the BglII site at the ends of the
plasmid DNA molecule integrated in the chromosome is
sometimes deleted.
It has been proved by the Southern analysis in
Example 15 that the number of copies of the L41 gene per
cell of Candida utilis is two. The number of copies of the
integrated plasmid was calculated by comparing the strength
2~6~~~7
5a
of the bands on the assumption that the 5.4 kb band
corresponds to the two copies of the L41 gene. The
densities of the bands were measured with an Imaging
Analyzer HAS 2000 (Fuji Film).
As a result, the number of copies of the plasmid
pCLRE2 was calculated to be in the range from 7 copies
(lane 1) to 25 copies (lane 3) in the ATCC 9256 strain,
from 3 copies (lane 5) to ll~copies (lane 6) in ATCC 9226
sirain. On the ether .hand, the number of copies was
calculated to be -.1? c:op~es ( lanes 9 and 10 ) in the ATCC
9950 strain.
These results indicate that transformants can be
obtained with the cycloheximide---re~ista.;~ce L41 gene in ATCC
9226 and ATCC 9256 strains as w~ X1.1 as the ATCC 9950 strain,
and that a plurality of pl«smids are integrated at the same
mime.
Example 14: TransformatioTi of Candida ut~l-is by
the lithium acetate method and the modified method thereof
The lithium acetate method (Ito et al., J.
Bacteriol., 153, 163-168 (1983)) has been extensively used
for the transformation of yeasts in Saccharomyces genus
because it is simple and easy in operation. Thus, Candida
utilis ATCC 9950 strain was tried to be transformed with
the plasmid pCLRE2 which was digested to be linear with
BglII according to the lithium acetate method and the
modified lithium acetate method in which ethanol or DMSO
was added (Soni et al., Current Cenet., 1993, 24, 455-459).
In the modified lithium acetate method, ethanol was added
after 10 minutes of the initiation of heat shock to the
cell suspension so that the final concentration is 10%, and
the mixture was incubated further for 10 minutes. DMSO was
also added together with a polyethylene glycol solution to
the cell suspension so that it has a final concentration of
(Os. After the cells were suspended in YPD solution and
cultured with shaking at 30~C for 4 hours, cells were
spread on the selectable plate containing cycloheximide and
.~.
21~8~37
59
incubated at a temperature of 28'C for 6 days.
As a result, 5 clones of the cycloheximide-
resistant strains were obtained with 2 ug of DNA of the
plasmid DNA by the modified lithium acetate method in which
ethanol DNA was added. Southern analysis was conducted with
chromosomal DNA prepared for 2 clones according to the
method described in Example 13. Bands derived from the
plasmid were observed and these clones were proved to be
. the transformants . The result indica tes that Candida uyilis
lC treated with lithium acetate also has an ability to .
integrate DNA, although the transformation frequency is
rather low as compared with the electric pulse method.
The experiment was conducted according to the
mE=.t-hod describet.;i by Soni et al . , but it is also possible to
improvF~ the transformation frequency by further examining
the treatmer~t conditions.
Example 15: Transformatvon with a target of
different rDNA region
1) Construction of plasmids
pCLRE4 and pCLRE5 were constructed by inserting the
3.5 kb EcoRI fragment obtained from pCRE2 (Figure 6), and
the 2.4 kb EcoRI fragment obtained from pCRE3 (Figure 6)
into the EcoRI site of the plasmid pCLBSl2 (Figure 15)
described in Example 9, respectively.
In addition, the 3 kb EcoRI-XbaI fragment and the
4. 5 kb EcoRI-XbaI fragment cut out from pCREl ( Figure 6 ) in
which a 7.5 kb EcoRI fragment containing rDNA was cloned
were ligated between the EcoRI and Xbal sites of
pBluescriptSK-, respectively. The XbaI site of each
plasmid was converted into the EcoRI site by inserting
EcoRI linkers (5'CCAAGCTTGG3') to construct plasmids pCRE6
and pCRE7. The 3 kb and 4.5 kb EcoRI fragments cut out from
these plasmids pCRE6 and pCRE7, respectively, were inserted
into the EcoRI site of a plasmid pCLBSI2 to construct
plasmids pCLRE6 and pCLRE7, respectively.
2168~~~1
The structures of the plasmids pCLRE4, pCLRE5,
pCLRE6 and pCLRE7 are shown in Figure 20.
2) Transformation
Each of the plasmids pCLRE4, pCLRE5, pCLRE6 and
5 pCLRE7 prepared was digested with a restriction enzyme into
a linear DNA. The ATCC 9950 strain was transformed with 1
ug of the DNA by the electric pulse method described in
Example 11. Transformat~.ons were conducted under the pulse
condition of electric capacitance of 25 ~,~F, voltage of '.5
?.0 KV/cm and resistance of 800 S2 with post-p~nlsP ru:~ture time
for 18 hours. Rest=fiction enzymes which were able to cut
sites found in rDNA fragments were employed. That is, the
rlasmid pCLRE4 was digested with BglII, pCLRE5 with RamHI .. _.
or X~aI, pCLRE6 with BamHI, and pCLRE7 with Apal or E;:~~RV,
1respectively. The plasmid pCLRE4 was also digested at the
i:lal site in the L41 gene to compare the difference of
transformation frequer_cies due to the difference of
integrated varget genes.
Two runs of the experiment were conducted. The
20 results are shown in Table 2.
Table 2: Transformation with plasmids pCLRE4,
pCLRE5, pCLRE6 and pCLRE7
Plasmid Number of transformants
per 1 ug of DNA
First Second
25 pCLRE4 (BglII) 786 593
pCLRE4 (Clal) 87 11
pCLRE5 (BamHI) 0 0
pCLRE5 (XbaI) 1 18
pCLRE6 (HamHI) 301 775
30 pCLRE7 (Apal) 409 754
pCLRE7 (EcoRV) 577 640
Digestion in the rDNA fragment of the plasmids
pCLRE4, pCLRE6 or pCLRE7 provided a high transformation
b
,.,
2.I6803'~
61
frequency, and several hundred transformants were obtained
per 1 ug DNA in either of the plasmids. On the other hand,
by the digestion of the plasmid pCLRE5 with either of BamHI
or XbaI, transformation frequency was very low as compared
with the cases of the other plasmids. This indicates that
transformation frequency varies largely depending on the
fragments used as targets of transformation even in the
rDNA region.
In addition, digestion of the plasmid pCLRE4 at the
ClaI site in the L41 gene, gave the transformation
frequency at about 1/10 - about 1/50 as compared with the
digestion at the BglII site in the rDNA. Furthermore,
Southern analysis described below indicates that the
plasmid molecule was integrated in the L41 gene locus when
it was digested at the ClaI site, and in the rDNA locus
when it was digested at the BglII site, respectively.
It has been revealed from these results that the
use of the rDNA having multiple number of copies in the
chromosome as a target leads to a high transformation
frequency.
3) Southern analysis
Cycloheximide-resistant strains were prepared with
pCLRE4 which had been digested with BglII or Clal, pCLRE5
which had been digested with Xbal, pCLRE6 which had been
digested with BamHI, and pCLRE7 which had been digested
with ApaI. Four strains were obtained with respect to each
plasmid. From these strains, chromosomal DNAs were
prepared. The DNA samples prepared were digested with
BglII or with BglII and NotI, and subjected to Southern
analysis with a 32P-labelled 1.8 kb HamHI-HindIII fragment
containing the L41 gene ( Figure 12 ) as a probe ( Figure 21 ) .
With respect to the strain in which the plasmid
pCLRE4 was integrated, by the digestion with BglII a 8.4 kb
band having the same size as the plasmid DNA which was
generated by the cut at the BglII site in the plasmid DNA
molecule was observed in addition to the 5.4 kb band
2~68~37
62
derived from the endogenous L41 gene ( Figure 21 ( 1 ) , lane 1-
8). Further, with respect to the strain in which the
plasmid digested with ClaI was integrated, 7.4 kb and 6.4
kb bands were observed in addition to the two bands as just
described ( lane 1-4 ) . The two bands were generated from the
presence of; the BglII sites in the plasmid molecules at
both ends of the integrated plasmid molecule and generated
by insertion of the plasmids at one of the chromosomal L41
genes locus; and BglII sites in the L41 gene. This
indicated that the plasmid molecules have been integrated
into the L41 gene locus by homologous recombination. The
results indicated that the plasmid molecules have been
integrated in the L41 gene locus when it was digested at
the ClaI site, and in the rDNA locus when it was digested
at the BglII site, respectively. This reveals that the
positions for integrating the plasmid can be selected
depending on the cutting site. Furthermore, sir_;.e in lanes
1 - 4, 5.4 kb, 7.4 kb and 6.4 kb bands have almost the
same density, the presence of 2 copies of the L41 gene in
the chromosome was proved.
In the strains in which the plasmids pCLRE5, pCLRE6
and pCLRE7 have been integrated, by BglII and NotI
digestion, some bands derived from the plasmids integrated
in the chromosome were observed in addition to the 5.4 kb
band derived from the endogenous L41 gene (Figure 21(2)).
Among them, bands having the same size with the plasmids
were observed, i . e. the 7 . 3 kb band for pCLRE5 ( lanes 1-4 ) ,
the 8 . 0 kb band for pCLRE6 ( lanes 5-8 ) , and 9 . 4 kb band for
pCLRE7 (lanes 9-12). These bands are generated from the
vicinal plasmids which have been integrated in tandem by
digestion with Notl which has only one cutting site in
these plasmid. Moreover, the 7 kb band in pCLRES ( lanes 1-
4), the 6.9 kb band in pCLRE6 (lanes 5-8), and the 11 kb
band in pCLRE7 ( lanes 9-12 ) were also observed. These sizes
are the same as the lengths of the fragment from the BglII
site in the rDNA locus to the NotI sites in the plasmid
DNAs obtained by BglII + Notl digestion when the plasmid
216037
63
DNAs have been integrated in the rDNA locus by homologous
recombination. This indicates that the plasmid DNAs have
been integrated at the cut sites in the chromosome by
homologous recombination.
The number of copies of the integrated plasmid was
obtained by comparing the densities of bands on the
assumption that the 5.4 kb bands in lanes 1-4 in Figure
21(1) correspond one copy of the L41 gene, the 5.4 kb bands
in lanes 5-8 in Figure 21(1) and in lanes 1-12 in Figure
21(2) correspond to two copies of the L41 gene. The density
of bands was measured with an Imaging Analyzer BAS200 ( Fuj i
Film).
It was revealed that from three copies (lane 4) to
five copies (lanes 1 and 3) of the plasmid pCLRE4 were
inserted in the L41 gene locus, and from two copies (lane
8) to eight copies (lane 5) in the rDNA locus. From this
result, it was observed that strains in which the plasmid
DNAs have been integrated in the rDNA locus with a higher
copy number tend to be selected. It is also suggested by
the fact that in the strains of Example 12 in which the
plasmid pCLRE2 has been integrated in the rDNA locus, the
number of copies of the plasmid DNA integrated were 6 to
15, while in the strain of Example 16 in which the plasmid
pCLRE2 has been integrated in the URA3 gene locus, the
number of the plasmid DNA integrated were about 3 to 4.
It was also revealed that from three copies ( Figure
21(2), lane 4) to five copies (lane 2) of the plasmid
pCLRES, from three copies (lane $) to six copies (lanes 5
and 6) of the plasmid pCLRE6, and from three copies (lane
12 ) to five copies ( lane 9 ) of the plasmid pCLRE7 have been
integrated, respectively.
Example 16: Integration of plasmid into the URA3
gene locus
Plasmid pCLURAl was constructed by inserting the 5
kb EcoRI fragment containing the URA3 gene (Figure 7) into
the EcoRI site of the plasmid pCLBSI2 (Figure 15). The
2~.~~fl3'~
64
plasmid was cut at the Pstl site in the URA3 gene locus.
the ATCC 9950 strain was transformed with this plasmid
according to the electric pulse method described in Example
11. Pulse was applied under the condition of an electric
capacitance of 25 uF, a resistance of 800 S2 and a voltage
of 5 KV/cm. Thus, forty cycloheximide-resistant colonies
per 1 ug DNA were obtained thereby.
Chromosomal DNAs were prepared for four clones
among the cycloheximide-resistant strains thus obtained.
The DNA thus prepared was digested with BglII or with SalI
+ Notl and subjected to Southern analysis. As probes, the
1.8 kb BamHI-HindIII fragment containing the L41 gene
(shown in Figure 12) for the DNA digested with BglII and
the 2.3 kb HindIII-EcoRI fragment containing the URA3 gene
(shown in Figure 8) for the DNA digested with SalI + NotI
were used after labelled with 32P.
The results are shown in Figure 22. 4~lith respect to
the parent strain ATCC 9950, when the URA3 gene was used as
a probe for the DNA digested with Sall + NotI, a 13 kb band
derived from the endogenous URA3 gene was observed (Figure
22(1), lane 1). On the other hand, with respect to the
resistant strain, in addition to the 13 kb band, a 10 kb
band generated from the NotI digestion of plural plasmids
tandemly integrated, and 8.4 kb and 14 kb bands generated
by the insertion of the plasmids at one of the URA3 genes
on chromosome were observed (lanes 2-5). These two bands
were generated from the presence of; the NotI sites in the
plasmid molecules at both ends of the integrated plasmid
molecules; and the SalI site in the URA3 gene region. This
indicated that the plasmid molecules have been integrated
in the URA3 gene locus by homologous recombination.
Furthermore, in the transformants, the 13 kb band
derived from the endogenous URA3 gene and the 8.4 kb and 14
kb bands derived from the plasmid molecules integrated in
the chromosome have almost the same densities. This
revealed that the number of copies of the URA3 gene is two
..~...,
65 2168037
copies per cell like the L41 gene, and that one copy in the
transformants has been disrupted by the insertion of the
plasmids. It has been also revealed by comparing these four
bands (14 kb, 13 kb, 10 kb and 8.4 kb) that the number of
the plasmid integrated were three copies ( lanes 3 and 5 ) or
four copies (lanes 2 and 4).
When the L41 gene is used as a probe for the DNA
digested with BglII, a 5.4 kb band derived from the
endogenous L41 gene was observed in the parent strain
IO ATCC9950. In addition to the 5.4 kb band, a 10 kb band
having the same size of the plasmid DNA was observed in the
resistant strains (lanes 2 - 5).
Example 17: Expression of a heterologous gene,
glucoamylase gene, in Candida utilis
(1) Construction of plasmids for expressing the
glucoamyla~a gene (STA1 gene)
A plasmid for expressing the STA1 gene was
constructed according to the procedure illustrated in
20 Figure 23.
The STA1 gene was first cloned from a genomic DNA
library of Saccharomyces diastaticus 5106-9A (a leu2, arg4,
STA1) (Yamashita and Fukui, Agric. Biol. Chem., 47, 2689-
2692) according to the following procedure. Chromosomal DNA
was prepared from the 5106-9A cell, partially digested with
Sau3AI and subjected to agarose gel electrophoresis to
prepare about 20 - 30 kb DNA fragments. The DNA fragments
and ~-phage vector EMHL3 digested with HamHI and then
dephosphorylated (Stratagene Cloning Systems) were ligated
30 with T4 ligase. The ligated mixture was in vitro packaged
with Gigapacx_TI*Gold Packaging Extract (Stratagene Cloning
Systems) to construct the genomic DNA library of the
chromosomal DNA.
Two oligonucleotides:
5'ACCACTATTACCACTACGGTTTGCTCTACA3' (SEQ ID NO: 19), and
5'GACACATCTCTGACGAGCATGACTTGGTTG3' (SEQ ID N0: 20)
which had been synthesized on the basis of the described
* Trade-mark
64409-4
..
r - ~ _ ___-
2.1~~~3'~
66
DNA sequence of a STA1 gene (Yamashita et al., J.
Bacteriol., 161, 567-573, 1985) were 32P-labelled at the
end with T4 kinase and used as a probe for screening about
20,000 plaques of the genomic DNA library. As a result, a
clone which was positive to either of the two probes was
obtained.
From the phage clone containing the STAl gene, a 4
kb BglII-HpaI fragment containing the STA1 gene was cloned
between the BamHI and HindIII of pUCl9 to construct the
plasmid pUSTAl (F:.gure 23).
Further, the plasmid pUSTAl was cut with a StuI
site present 5 by downstream of the initiation codon ATG,
and the following synthetic adapter (SEQ ID NO: 21)
containing a Xbal site and an initiation codon:
5'-CTAGATGGTAGG-3'
3'-TACCATCC-5'
was ligated. Then, partial digestion of the plasmid with
SalI gave the STA gene as a 2.7 kb XbaI-Sall fragment.
Furthermore, pUCl2 was digested with Pstl and
HindIII, treated with T4 DNA polymerise, and BglII linkers
were ligated to construct a plasmid pUC12Bg1II. The 2.7 kb
Xbal-SalII fragment containing the STA1 gene was inserted
between the Xbal and SalII of the plasmid pUCI2BgII to
construct a plasmid pUSTA2.
The 2.7 kb Xbal-BglII fragment was cut out from the
plasmid STA2 and inserted between the Xbal and BamHI sites
of the expression vector pPGKPT4 to construct a plasmid
pGKSTAl.
Furthermore, a 4.9 kb Notl fragment containing the
PGK gene promoter, the STA1 gene and the PGK gene
terminator was cut out from the plasmid pGKSTAl. The
fragment was inserted into the NotI site of the plasmid
pCLBSI2 to construct a plasmid pCLSTAl, and into the NotI
site of the plasmid pCLRE4 to construct a plasmid pCLRSTAl,
respectively.
(2) Transformation of Candida utilis and
21fi~~37
67
glucoamylase expression
ATCC 9950, ATCC 9226 and ATCC 9256 strains were
transformed with the plasmid pCLRSTAl digested with BglII
according to the electric pulse method described in Example
11. Pulse was applied under the condition of electric
capacitance of 25 pF, resistance of 1, 000 S~, and voltage of
3.75 KV/cm or 6.25 KV/cm
Cycloheximide-resistant colonies were obtained in
either of the strains although frequencies were different
depending on strains.
Glucoamylase activity was examined for two strains
of each of the transformants on a plate containing starch
as a substrate (3o Soluble starch (Katayama). 20
polypeptone, to yeast extract, 3.3 x 10 3a Bromocresol
purple, 2% Bacto agar). As a result, for all of the
transformants derived from the three strains halos due to
secrPtPd glucoamylase were observed. Thus, the expression
of the gene were confirmed. In addition, the A'z'CC 9950
strain was transformed with an AflII digested plasmid
pCLSTAl. When the expression of the glucoamylase gene
integrated at the L41 gene locus was further examined, the
formation of halos was observed as well.
Furthermore, the glucoamylase activities of these
transformants were measured. The cells were cultured in YPD
liquid medium overnight, and the supernatant was used as a
crude enzyme solution. The reaction was conducted in 500 u1
of a reaction solution containing 400 u1 of the crude
enzyme solution, 0.5% soluble starch and 100 mM sodium
acetate ( pH 5 . 0 ) at 50'C for 20 minutes . After reaction,
the enzyme was inactivated by heat treatment at 100'C for
5 minutes, and the concentration of glucose generated was
determined with a commercially available kit (Glucose B-
Test (Wako Pure Chemical Industries, Ltd.)).
The activity of glucoamylase was defined as 1 unit
when the amount of glucose isolated under the reaction
condition is 100 ug. The values of the activity per 1 ml
21~8~3~
68
supernatant of the culture are shown in Table 3.
Table 3: Glucoamylase activities of the Candida utilis
yeasts transformed with plasmids pCLSTAl or pCLRSTAl
Plasmid Glucoamylase
activity
(units/ml)
ATCC 9256
ATCC 9266
ATCC 9950
pCLRSTAl(BglII) 11.3 7.9 8.3
pCLRSTAl(BglII) 10.5 6.6 8.5
pCLSTAl(AflII) - - ~6
pCLSTAl(AflII) - - 8-8
-DNA 0.0 0.0 0
Activities were measured on two independent transformed
strains.
- . no measurement.
It was revealed that the signal sequence of
glucoamylase protein was recognized and the enzyme was
secreted into medium in the ATCC 9950, 9226, and 9256
strains, although glucoamylase is a heterologous protein
derived from Saccharomyces diastaticus.
Moreover, Two ATCC 9950 strains transformed with
each of the plasmid pCLSTAl digested with BglII or the
plasmid pCLSTAl digested with AflII were cultured in YPD
liquid medium containing 40 ug/ml cycloheximide and 50
glucose at 30cC for 4 days. A 10 u1 portion of the cultured
medium was subjected on 4 - 20~ SDS polyacrylamide gel
electrophoresis to analyze the proteins in the culture
(Figure 24). The gel was stained with Coomassie brilliant
blue. As a control, culture medium of the strain
transformed with the BglII digested plasmid pCLRE2 was
analyzed (lane 1). An about 100 kDa protein corresponding
to glucoamylase was observed in either cultures, and the
amount of the protein was estimated at about 2 - 5 ug from
216~~~~
69
the densities of the stained bands . This indicates that the
glucoamylase gene has been expressed at a high level and
has been secreted in the medium. It has been thus revealed
that Candida utilis can be used as an appropriate
host/vector system for producing secretory proteins.
Example 18: Expression of a heterologous gene,
(lacZ gene), in Candida utilis
(1) Construction of plasmids for expressing la~~Z
gene
- Plasmids for expressing the lacZ gene were
constructed according to the procedure illustrated in
Figure: 25 .
Firstly, the lacZ gene encoding (3-galactosidase was
cut out as a 3.1 kb BamHI fragment from plasmid pMC1871
(Pharmacies). 'ihe fragment was ligated to the BglII site of
a plasmid YFpl3K (Sone et al.. Appl. Environ. Microbiol.,
54, 38-42 (1988)) to select a plasmid pZ4 having a HindIII
site at the 5' side of the gene.
A lacZ gene having an initiation codon ATG was cut
out as a 3.1 kb HindIII-Xhol fragment from the plasmid. The
fragment was then ligated between the sites of HindIII and
Xhol in pBluescript SK- to construct a plasmid pLACZl.
This plasmid was digested with HindIII + XbaI,
subjected to Klenow treatment, and recyclized to construct
a plasmid pLACZ2.
Furthermore, the lacZ gene was cut out as a 3.1 kb
XbaI-KpnI fragment from the plasmid, and ligated between
the sites of XbaI and KpnI in the plasmid pPGKPTS (Figure
4) to construct a plasmid pGKLACl.
In addition, a 5.4 kb Notl fragment containing the
PGK gene promoter, the lacZ gene and the PGK gene
terminator was cut out from the plasmid pGKLACl, and
inserted into the Notl site of the plasmid pCLBSI2 and the
Notl site of the plasmid pCLRE4 to construct plasmids
pCLLACl and pCLRLACl, respectively.
70
(2) Transformation of Candida utilis and the
confirmation of ø-galactosidase activity
The ATCC 9950 strain was transformed with the
plasmid pCLRLACl digested with BglII or the plasmid pCLLACl
digested with AflII by the electric pulse method described
in Example 11. Two strains of each of the transformed ATCC
9950 strains were cultured up to logarithmic growth phase
( OD600 = about 2 - 3 ) in 5 ml of YPD liquid medium for 6
hours. ø-Gslactosidase activity was measured according to
tt;e method described in Methods in Yeast Genetics - A
Laboratory Course Manual - Rose, M.D. et al., p. 155 - 159,
Cold Spr~.ng Harbor Laboratory Press, NY (1990).
Specifi,-.;ally, after the collected cells were suspended in
1 ml of <:, buffer, 3 drops of chloroform and 2 drops of 0.1%
SDS were added, and the mixture was vortexed for 10
seconds. After incubation at 28'C for 5 minutes, 0.2 ml of
ONPG solution was aided, and the mixture :nas incubated for
further 10 minutes. Then, 0.5 ml of Na~C03 solution was
added to stop the reaction. After the measurement of OD420~
the ø-galactosidase activity was calculated according to
the equation. The ø-galactosidase activity was defined as
1 unit when ortho-nitrophenol is produced in an amount of
1 nmol at 28~C for 1 minute. The activities of the cells
obtained per OD600 are shown in Table 4.
2~68~3'~
71
Table 4: ~i-galactosidase activities of the ATCC 9950
strains transformed with the plasmids pCLLACl or pCLRLACl
Plasmid ~3-galactosidase activity
( units/OD600 )
pCLLACl (AflII) 6.4
pCLLA~l (AflII) 6.7
pCLRLACI (BglII) 6.8
pCLRLACI (BgII~T) 7.0
-DNA 0.1
From the result, it ',>~,s _='onfirmed that both of the
ATCC 9950 strains transformed with the plasmids pCLRLACl or
pCLLACl showed the activity, indicating the lacZ gene
derived from E. coli was expressed and ac;:iT,re ~i-
galactosidase was produced in Candida utilis. It has been
known that the leucine codon CUG is translated into serine
in some yeasts of the Candida genus such as Candida maltosa
or _C. albicans (Ohama et al., Nucleic Acids Res., 21, 4039
- 4045, 1993), so that the lacZ gene derived from E. coli
is not translated into an active ~i-galactosidase (Sugiyama
et al., Yeast, 11, 43 - 52 (1995)). In this Example, active
~i-galactosidase is produced in Candida utilis, and it has
been shown in Example 17 that glucoamylase is produced in
a high amount. It is thus believed that Candida utilis can
be used as a host for expressing heterologous genes.
Example 19: Expression of a heterologous gene (APT
gene) in Candida utilis
(1) Construction of plasmids for expressing the
APT gene
Plasmids for expressing the APT gene were
constructed according to the procedure illustrated in
Figure 26.
a
2~68~3'~
72
Firstly, a 1.1 kb XhoI-PstI fragment was cut out
from plasmid pUC4K (Pharmacia) containing aminoglycoside
phosphotransferase derived from transposon Tn903 (APT gene)
and inserted between SalI and PstI of pUCl9 to construct a
plasmid pAPHl.
After the plasmid pAPHl was digested with PstI and
treated with T4 DNA polymerise to form blunt ends, BglII
linkers (5'CAGATCTG3') were inserted to form a plasmid
pAPH2.
Furthermore, the APT gene was cut out as a 1.1 kb
XbaI-BglII fragment from the plasmid pAPH2 and inserted
between the XbaI and BamHI sites.of the expression vector
pPGKPT4 (Figure 4) to construct a plas~:id pGKAPHl.
In addition, a 3.3 kb NotI fragment containing the
PGK gene promoter, the APT gene and the PGK terminator was
cut out from the plasmid pGKAPHl. 'i'his fragment was then
inserted into the Notl site of the p~asmids pCLBSl~ anal
pCLRE4 to construct plasmids pCLAPHl and pCLRAPHl,
respectively.
(2) Transformation of Candida utilis and
confirmation of resistance to 6418
ATCC 9950, ATCC 9226 and ATCC 9256 strains were
transformed with the plasmid pCLRAPHl digested with BglII
according to the electric pulse method described in Example
11. Pulse was applied under the condition of electric
capacitance of 25 uF, resistance of 1, 000 S2, and voltage of
3.75 KV/cm or 6.25 KV/cm.
As a result, cycloheximide-resistant colonies were
obtained in either of the strains although frequencies were
different depending on strains. The growth of cells was
examined for two strains of each of the transformants on
YPD plates containing various concentrations of 6418. As a
result, the growth of the transformants was confirmed for
all of the three strains of Candida utilis, and it
indicates that the APT gene has expressed in these
transformants.
In addition, the ATCC 9950 strain was transformed
. ~ 2~6~03'~
73
with an AflII digested plasmid pCLAPHl in order to examine
the expression of genes integrated at the L41 gene locus.
As a result, the growth of transformants was confirmed for
the strain, and expression was also confirmed on the APT
gene integrated at the L41 gene locus.
(3) Stability of the integrated plasmid
The stability of the integrated plasmid DNA was
examined in the following procedure for two ATCC 9950
strains transformed with each of the plasmid pCLRAPHl
digested with BglII or the plasmid pCLAPHl digested with
AflII. The transformant was first cultured up to the
stationary phase in 5 ml of YPD liquid medium containing 40
ug/ml cycloheximide. The generation number at the time laas
referred to as zero. Then, a 5 u1 portion of tree cell
culture was inoculated in 5 ml of YPD liquid medium arid
cultured up to the stationary phase. The generation number
at the time was referred to ten. The procedure was repeated
to culture the cells up to the 20th generation. T~~~e
stability of the plasmid was calculated by spreading the
diluted the cell suspension on YPD plate and YPD plate
containing 40 ug/ml cycloheximide, culturing the plate at
30°C for 2 days and counting the colonies
The results are shown in Table 5.
Table 5: Stability of plasmid DNA integrated in the
chromosome of ATCC 9950
Plasmid Retention rate (%)
pCLRAPHl (BglII) 91.3
pCLRAPHl (BglII) 878
pCLAPHl (AflII) 9g5
pCLAPHl (AflII) 936
It has been confirmed from the result that the DNA
,.....
2168037
74
fragments inserted in an rDNA locus and in the L41 gene
locus are stable.
Example 20: Selection of Candida utilis
transformants using the 6418-resistance as a selectable
marker
The plasmid pCLRAPHl contains the mutated L41 gene
conferring resistance to cycloheximide and the APT gene
conferring resistance to 6418 as selectable markers for
l0 transformants. Since the APT gene has been conf~.rmed to be
expressed by the PGK gene promoter, direct selection of
transformants by resistance to 6418 was tried.
The plasmid pCLRAPHl was digested with BglII t~
form a linear plasmid. The ATCC 9950 strain was transf~~r_med
with the linearized plasmid by the electric pulse method
described in Example 11. Pulse was applied under the
condition of electric capacitance of 25 uF, resistance of
1,000 n, and voltage of 5 KV/cm. The cells were cultured in
YPD medium containing 1 M sorbitol for 6 hours, and spread
on YPD plate containing cycloheximide and on YPD plate
containing 150 ug/ml 6418.
The results are shown in Table 6.
Table 6: Selection of ATCC 9950 transformants with the
plasmid pCLRAPHl by different drug-resistance markers
6418 Cycloheximide
Plasmid 1, 000 S2 800 S2 1, 000 S2 800
pCLRAPHl (BglII) 100 111 7 18
-DNA 0 - 0 -
* Number of transformants per 0.1 ug DNA;
* The concentration of 6418 and cycloheximide was set as
150 ug/ml and 40 ug/ml, respectively.
. not measured.
75
It is shown from the result that the number of
colonies selected by resistance to 6418 is 10 times larger
than that selected by resistance to cycloheximide.
Chromosomal DNA was prepared for 4 colonies
selected by resistance to 6418 and 4 colonies selected by
resistance to cycloheximide. The DNA thus prepared was
digested with BglII + NotI, and subjected to Southern
analysis with the 32P-labelled 1.8 kb BamHI-HindIII
fragment ~con~:aining the L41 gene as a probe ( Figure 27 ) . As
a ~~esu~,t, a 4.4 kb band derived from the nlasmid was
. observed in addition to the 5.4 kb band derived from the
endogenous L4l,gnne. The densities of bands were measured
with an Imaging A~a~yzer BAS 2000 (Fuji Film). The number
of copies of. t?.ze integrated plasmid was calculated by
comparing the band derived from the plasmid with the band
derived from the endogenous L41 gene (2 copies/cell). It
has been indicated tnat the plasmid~ were present from four
(lane 2) to sevem.copi.es (lane 5) in the strains selected
by resistance to cycloheximide. It has been also calculated
that the plasmids were present in one copy (lanes 6-9) in
all of the four strains selected by resistance to 6418.
These results indicate that strains in which a plurality of
plasmids have been integrated can be easily obtained, while
the frequency of transformation becomes low when the
mutated L41 gene was used as a marker for selecting the
transformants.
Furthermore, the plasmid pGKAPH1 was digested with
Notl and divided into two fragments. That is, the plasmid
was divided into a fragment containing the PGK gene
promoter, the APT gene and the PGK gene terminator, and a
vector fragment. With these fragments, ATCC 9950 strain was
transformed. Pulse was applied under the condition of
electric capacitance of 25 uF, resistance of 1,000 S2, and
voltage of 5 KV/cm. When transformants were selected on YPD
plate containing 200 ug/ml 6418, 156 transformants were
obtained on the basis of 1 ug of DNA. This indicates that
76
in the Candida utilis yeast, the transformation by gene
replacement is also observed in addition to the
transformation by gene insertion with the plasmid pCLRAPHl
linearized by the digestion with HglII. It is also revealed
that transformation by gene replacement happens
efficiently, since the frequency of transformation was
relatively high.
~16~03'~
77
Example 21: Shortening of PGK gene promoter and
identification of minimal functional region
The PGK gene promoter used in Examples 17 - 20 was
tried to be shortened for identifying the minimal
functional region of the promoter.
First, five fragments containing PGK gene promoters
different in length, the APT gene and the PGK gene
terminator were obtained with use of the restriction enzyme
sites i.n the PGK gene promoter fragment of the plasmid
pGKAPHl described in Example 19. That is, the plasmid
pGKAPHl was digested with NotI, Sacl, EcoRI + SacI or PstI
+ SacI to prepare four fragments. The plasmid pGKAPHl was
digested with SphI, and treated wits T4 DNP, polymerase to
form blunt ends. HamHI linkers ( 5' f.CGGATCCGG3' : SEQ ID NO:
22) were added, and digestion with BamHI and Notl was
conducted to obtain another fragment.
Of the 0.7 kb and 5.8 kb fragmer:;.s obtained by
digesting the plasmid pCRE2 described in Example 5 with
HindIII, the 5.8 kb fragment was recyclized by ligation to
form a plasmid pCRE8 ( Figure 28 ) . The plasmid pCRE8 was
digested with Notl, BamHI + NotI, SacI, EcoRI + Sacl or
PstI + SacI, ligated with the above described fragments to
construct plasmids pCRAPH2, pCRAPH3, pCRAPH4, pCRAPH5 and
pCRAPH6 (Figure 28). The PGK gene promoter fragment
contained in each of the plasmid had a length of 1.35 kb in
pCRAPH2, 0.83 kb in pCRAPH3, 0.46 kb in pCRAPH4, 0.40 kb in
pCRAPH5 and 0.16 kb in pCRAPH6.
After each of the plasmids pCRAPH2, 3, 4, 5 and 6
thus constructed was linearized by digestion with BaglII,
they were used for transformation of the ATCC 9950 strain
according to the electric pulse method described in Example
11. Pulse was applied under the condition of electric
capacitance of 25 uF, resistance of 1,000 ~2, and voltage of
5 KV/cm.
Transformants were selected on a YPD plate
containing 200 ug/ml 6418. When the plasmids pCRAPH2,
pCRAPH3, pCRAPH4 and pCRAPHS were used, about 300
78
transformants were obtained on the basis of 1 ug of DNA
with each plasmid. However, no transformant was obtained
with the plasmid CRAPH6. This indicates that the fragment
containing the region from the nucleotide immediately in
front of the initiation codon ATG of the PGK gene to the
Pstl site at 169 by upstream of 5' end has no function as
a transcriptional promoter, but the fragment containing up
to the .EcoRI site at -4U1 by upstream and further longer
region teas a function us a transcriptional promoter.
Therefore, in the 1346 h~ ~eqLerce containing the PGK gene
promoter shown in Figure 3, the 401 by sequence from the
946th EcoRI site to the 1346th nucleotide immediately in
front of ATG contains a sequence required fir the promoter
function.
Example 22: Cloning of the glyceraldehyde-3-
phosphate dehydrogenase (GAP) gene and sequt~-~cing the DNA
sequence of a DNA fragment containing the GAP gene
The cloning of glyceraldehyde-3-phosphate
dehydrogenase (GAP) gene in Candida utilis was conducted
with the genomic DNA library of Candida utilis constructed
in Example 2 as a DNA library by the hybridization method
with a known GAP gene of the other organisms as a probe.
Filters having adsorbed phase DNA of about 20,000 plaques
of the above described library thereon were prepared
according to the method described in Molecular Cloning, 2nd
edition, p. 2, 95 - 121, Cold Spring Harbor Laboratory
(1989). On the other hand, an about 1 kb AsuII-AflII
fragment was cut out from a derivative plasmid of pUCl8
which retains a 2.1 kb HindIII fragment containing the GAP
gene of Saccharomyces cerevisiae (Yamano et al., Journal of
Biotechnology, 32, 165-171 (1994)) as a fragment comprising
almost of the GAP gene. The fragment was 32P-labelled, and
hybridization was conducted with the labelled fragment as
a probe. Three positive plaques were isolated. A phage DNA
prepared from one of these plaques was subcloned and a 6.5
v
.r..
79
kb EcoRI fragment contained in the phage DNA was isolated.
The fragment was then inserted in the EcoRI site of the
plasmid vector pBluescript IISK+ to construct plasmids
pGAPl and 2 (Figures 29).
The isolated 6.5 kb EcoRI fragment was digested
with restriction enzymes HindIII, Clal, Smal or SpeI alone
or in combination, and Southern hybridization was conducted
on the resulting fragments with the GAP gene of
Saccharomyces cerevisiae as a probe. Strong,hybridi,z.ation
was observed with the 3.8 kb HindIII-Spel fragment. T.he 3.8
kb HindIII-Spel fragment was inserted between the sites of
HindIII and Spel of plasmid vectors pBluescript IISK+ or
pBl::=script IIKS+ to prepare plasmids pGAPl and pGAP2,
respectively. Deletion mutants at the restriction enzymE~-
sites such as HindIII, ClaI or SmaI of these plasmids were
prepared, and continuous deletion mutants were prepared
wia:~. ExoIII and mung bean nuclease in order to prepare
t:~lasmids having a variety o~ deletion mutations and the
sequence of the 3749 by HindIII-SpeI fragment was
determined (Figure 29).
When the expected structural gene region was
analyzed, a 1005 by open reading frame was observed. With
respect to the amino acid sequence of a gene product
deduced from the frame, homology to the GAP gene product of
Saccharomyces cerevisiae was examined. These sequences
showed 79.6°s of homology to each other, so that the
isolated gene was concluded to be the GAP gene of Candida
utilis. Further, the fragment contains a 975 by sequence
upstream of the initiation codon and a 1769 by sequence
downstream of the termination codon as a regulatory region.
The 975 by sequence ranging from the HindIII site to
immediately in front of the initiation codon ATG which is
anticipated to contain the transcriptional promoter is
shown in Figure 30. Further, the 802 by sequence ranging
from immediately behind the termination codon TAA to the
AfIIII site which is anticipated to contain the
transcriptional terminator is shown in Figure 31.
k
2~6803'~
Example 23: Construction of expression vectors
with the promoter and terminator of the GAP gene
DNA fragments containing either of the promoter or
the terminator were obtained from the GAP gene regulatory
5 regions of Candida utilis by the PCR method (Figure 29).
As the promoter, a fragment ranging from the
HindIII site to immediately in front of the initiation
codon ATG was obtained with the plasmid pGAPl as a
template. As the primers, the two sequences .
10 5' -CCAAGCTTACAGCGAGCACTCAAATCTGCCC-3' ( SEQ ID r.10 : 23 ) , r nd
5'-CCTCTAGATATGTTGTTTGTAAGTGTGTTTTGTATC-3' (SEQ ID NO: 24)
were used. The promoter was synthesized to have the Xbal
sire ~:~ich was located immediately in front of the
initiation ~:odon at the 3' downstream side.
15 Further, as the terminator, a fragment from
immediately aftar the terming Lion codon to the Spel site
was c~wined from the pJ_asmid pGAPl as the template. As the
pr~.;ners, the sequences:
5'-GGGATCCATTGTATGACThTTATTTATGGG-3' (SEQ ID NO: 25), and
20 5'-GGACTAGTGAGATGACTCTAGGCATCTTCT-3' (SEQ ID N0: 26)
were used. The terminator was synthesized to have the BamHI
site which was immediately after the termination codon at
the 5' side.
The PCR process was conducted 30 cycles with a Pfu
25 DNA polymerase (Stratagene). The promoter fragment
synthesized by the PCR process was digested with HindIII
and XbaI, inserted between the sites of HindIII and Xbal of
a pUCl9 vector to construct a plasmid pUGpro (Figure 32).
On the other hand, the terminator fragment was digested at
30 the AfIIII site of the about 0.8 kb downstream of the
termination codon, treated with Klenow enzyme to form blunt
ends, and digested with BamHI. The 0.8 kb fragment thus
obtained was inserted between the BamHI and Smal sites of
the pUCl9 vector to construct a plasmid pUGter ( Figure 32 ) .
35 After the EcoRI site at the downstream end of the
GAP terminator of the plasmid pUGter was treated with
Klenow enzyme to form blunt ends, NotI linkers (5'
216803'
81
AGCGGCCGCT3': SEQ ID NO: 18) were isolated to construct a
plasmid pUGterN. Further, a 0.95 kb GAP promoter fragment
was cut out from the plasmid pUGpro with HindIII and XbaI,
and inserted between the sites of HindIII and XbaI of the
pUGterN to construct an expression plasmid pGAPPTl.
Moreover, the HindIII site at the upstream end of the
promoter was treated with Klenow enzyme to form blunt ends,
and ligated to Notl iirikers ( 5' AGCGGCCGCT3' : SEQ ID NO: 18 )
to construct a;plasmic; pGAPPT2 (Figure 32).
~ In order to confirm that the expression plasmid
pGAPPT2 thus constructed functions practically in Candida
utilis, a 1.1 kb APT gene fragment cut out with Xbal and
BglII from the pla~mid pApu2 described in Example 19 was
inserted between t~:e sa.tes of Xb~I and BamHI of the plasmid
pGAPPT2 to construct a ~plasmid pGAPAPHl (Figure 32).
After the plasmid pGAt~AF~Hi thus constructed was
digested with NotI, it wa:_ used for transformation of the
ATCC 9950 strain by the electric pulse method under the
pulse condition of electric capacitance of 25 ~aF,
resistance of 1,000 S~, and voltage of 5 KV/cm.
Transformants were selected on a YPD plate containing 200
ug/ml 6418. About 40 transformants were obtained with 0.1
ug of DNA. This indicated that the promoter and terminator
of the GAP gene were active.
Example 24: Cloning of the plasma membrane proton
ATPase (PMA) gene and sequencing the DNA sequence of a DNA
fragment containing the PMA gene
Cloning of the plasma membrane proton ATPase (PMA)
gene in Candida utilis was conducted by the hybridization
method using the genomic DNA library of Candida utilis
constructed in Example 2 and a part of the known PMA gene
of the other organisms as a probe. Filters having adsorbed
phase DNA of about 20,000 plaques of the above gene library
thereon were prepared according to the method described in
Molecular Cloning, 2nd edition, p. 2, 95 - 121, Cold Spring
Harbor Laboratory (1989). An about 1 kb region
.....
82
corresponding to +1 - +1027 (A of the initiation codon ATG
is referred to as +1) of the 5' end of a PMA1 structural
gene was amplified with the two primers:
5'-ATGACTGATACATCATCCTCTTCATC-3' (SEQ ID NO: 27), and
5'-TAACGACAGCTGGCAAACCGACTGGGAC-3' (SEQ ID NO: 28)
which were synthesized from the DNA sequence of PMA1 gene
of Saccharomyces cerevisiae (Serrano et al. Nature 319,
689-69:x(1986)) with the chromosomal DNA of .. the
Saccharomyces . cArevisi=.te AH22 strain as the template
.
accordir.a ... ~-o t he PCR method . The chromosomal DNA has
prepared according to the method described in Methods in
Yeast Genetics - A Labor~finry Course Manual - Rose, M.D. et
al., p. 126 - 127, Cc.ld SpF~~g Harbor Laboratory Press, NY
(1990). The fragme~~-. ~.~btained was 32P-labelled, and
hybridization was conduci;ed with the labelled fragment as
a probe. As a result, four positive plaques were obtained.
For a phage DNA of one of the four positi=,:e claques, the
insert DNA was digested w~.th XbaI to isolate four 10 k:b, 4
kb, 2.8 kb and 2.6 kb Xbal fragments.
When the four isolated fragments were hybridized
with a probe of an about 1 kb fragment of the PMA1 gene of
Saccharomyces cerevisiae used for screening, the probe was
hybridized with a 2.6 kb XbaI fragment. The fragment was
inserted in the XbaI site of the plasmid vector pBluescript
IISK+ to prepare plasmids pPMAFl and pPMAF2 which have been
inserted in the opposite directions to each other (Figure
33).
From these plasmids, deletion mutants at the
restriction enzyme sites such as BamHI, ClaI or EcoRI of
these plasmids were prepared, and deletion mutants were
prepared with exonuclease III and mung bean nuclease in
order to prepare plasmids having a variety of deletion
mutations and to determine the DNA sequences of about 1 kb
from the both ends (Figure 33). When the expected
structural gene region was analyzed, a 352 by open reading
frame which showed about 50~ of homology to the 5' terminal
83
region of the PMA1 structural gene of Saccharomyces
cerevisiae was observed within about 1 kb sequence
containing the region from the Xbal site to the EcoRV site
of the left side in Figure 33. Within about 0.8 kb sequence
containing the region from the XbaI site at the other side
to inside including the BamHI site, a 754 by open reading
frame which shows 70% of homology to the range from +1292
to +2046 (A.of the initiation codon ATG is referred to as
+1) of the P~~IA1 gene of Saccharomyces cerevisiae was
observed. It was judged frora fi?~i:~ result that the isolated
gene is-the PMA gene of Candida utilis. Further, the 2.6 kb
XbaI fragment contained a 599 by sequence upstream the
initiation codon ATG. The sequence of the 599 br r~agment
which is expected to contain the transcriptional promc4er
is shown in Figure 34.
As for the transcriptional terminator, tile
remaining three fragments cut out from the same ~:~iagP. DNA
with Xbal ( ~0 kb, 4 kb and 2. 8 kb ) were subc:loned, and
their DNA sequences were determined from the both terminal
sides to examine their homology to the region of the 3'
side of the PMA1 gene of Saccharomyces cerevisiae. It has
been revealed that a region which shows high homology to
the 3' terminal side of the PMAl gene is present at the one
side of the 2.8 kb XbaI fragment. The XbaI fragment was
inserted in the Xbal site of the plasmid vector
pBluescriptIISK+ to prepare plasmids pPMALl and pPMAL2 in
which the fragment was inserted in opposite direction to
each other (Figure 33). Plasmids having a variety of
deletion mutations were prepared from these plasmids by
digestion with Kpnl or with use of exonuclease III and mung
bean nuclease, and the 1.9 kb DNA sequence from the Xbal
site to the Kpnl site was determined (Figure 33). This DNA
sequence comprises a 717 by open reading frame which has a
homology of about 82% to the range from +2041 to +2757 (A
of the initiation codon ATG is referred to as +1) of the
PMA1 gene of Saccharomyces cerevisiae and a 188 by sequence
downstream the termination codon TAA. The 1188 by sequence
2168~3'~
84
from immediately after the termination codon TAA to the
KpnI site which is expected to contain the transcriptional
terminator is shown in Figure 35.
Example 25: Construction of an expression vector
with the promoter and terminator of the PMA gene
First, DNA fragments containing the promoter or the
terminator were obtained from the PMA gene regulatory
regions of Candida utilis by th~~PCR method (Fygure 33).
As the promoter, a fragment ranging. from the
location at 20bp downstream of the Xbal site to immediately
in front of the initiation codon ATG was obtained with the
plasmid pPMAFl as a template. The two DNA se'quencP~::
5'-GGCGGCCGCAATTAACCCTCACTAAAGGGAACGA-3' (::FQ TD NO: 29:)
and
5'-TTCTAGACTATATCAATGGTTAGTATCACGTG-3' (SEQ ID NO: 30)
were ~a ed as t~~2 primers. The promoter was synth'sized to
have the Notl site which was located at the 5' upstream end
and the XbaI site which was located at immediately in front
of the 3' downstream initiation codon.
As the terminator, a fragment ranging from
immediately after the termination codon TAA to 403 by
downstream the termination codon with the plasmid pMALl as
a template. The DNA sequences:
5'-CCGGTACCTAAGCCGCTAATACCCC-3' (SEQ ID NO: 31) and
5'-GGGCGGCCGCACTCGCTGATCGAAA-3' (SEQ ID N0:32)
were used as the primers . The terminator was synthesized to
have the KpnI site which was located immediately after the
termination codon at the 5' upstream side and the Notl site
which was located at the 3' downstream end.
The PCR process was conducted 30 cycles with Pfu
DNA polymerase (Stratagene). The promoter fragment
synthesized by the PCR process was digested with NotI and
Xbal, inserted between the NotI and XbaI sites of
pBluescriptIISK+ vector to construct a plasmid pBMpro. On
the other hand, the terminator fragment was inserted
ms~a3~
between the KpnI and Notl sites of the pBluescriptIISK+ to
construct a plasmid pBMter. The 0.4 kb KpnI-NotI fragment
obtained from the plasmid pBMter was inserted between the
sites of Kpnl and NotI of the plasmid pUCl9N which was
5 constructed by subjecting the EcoRI site of the plasmid
pUCl9 to the Klenow enzyme treatment and ligating Notl
linkers (5' AGCGGCCGCT 3': SEQ ID NO: 18) to construct a
plasmid pUMter (Figure 36).
The 0.4 kb terminator fragment obtained by
10 digesting the plasmid pUMter with XbaI and NotI and the
0.65 kb promoter fragment obtained by digesting the plasmid
pHMpro with Notl and XbaI were ligated with the 2.9 kb
fragment obtained by digesting the plasmid pPGKPT5
constructed in Example 4 with NotI to construct a plasmid
15 pMAPHl (Figure 1).
In order to confirm that the expression plasmid
pMAPHl thus constructed functions practically in Candida
utilis, the 1.1 kb APT gene fragment cut out with Xbal and
BglII from the plasmid pAPH2 described in Example 19 was
20 inserted between the sites of XbaI and BamHI of the plasmid
pMAPHl to construct a plasmid pMAAPHl (Figure 36).
After the plasmid pMAAPHl thus constructed was
digested with Notl, it was used for transformation of the
ATCC 9950 strain by the electric pulse method under the
25 pulse condition of electric capacitance of 25 uF,
resistance of 1,000 n, and voltage of 5 KV/cm.
Transformants were selected on a YPD plate
containing 200 ug/ml 6418. About 40 transformants were
obtained with 0.1 ug of DNA. This indicates that the
30 promoter and terminator of the GAP gene were active.
Example 26: Cloning of DNA fragments containing
autonomously replicating sequences (ARS)
The 3.3 kb Notl fragment containing the PGK gene
35 promoter and the PGK gene terminator was cut out from the
plasmid pGKAPHl constructed in Example 19, and inserted
into the Notl site of the plasmid pBluescripIISK
21~803'~
86
(Stratagene) to construct a plasmid pGKAPH2 (Figure 37).
Then, 200 ng of the plasmid pGKAPH2 having been digested
with BamHI and dephosphorylated and 200 ng of 3 - 7 kb
fragments digested partially with Sau3AI of the genomic DNA
of the Candida utilis ATCC 9950 strain obtained in Example
2 were ligated with T4 DNA ligase. E. coli DH5 was
transformed with the DNA solution, and plasmid DNA mixtures
were extracted from about 30,000 transformants obtained
from the: genomic DNA library. The ATCC 9950 strain was. . ,-_
trGnsforTned with 3 ug of the DNA prepaxed from the lii~.rary
according to the electric pulse method described in Example
11 under the 4 conditions of an electric capacitance of 25
uF, a resist.-?-ice of 800 n or 1,000 S2 and a voltage of 3.75
KV/c=.;~~ or. 5 KV/cra. Thus, seven cycloheximide-resistant
colonies were obtained. These resistant strains were
cultured in YPi~ medium containing 400 ug/ml of 6418. Total
DNA was pre~~sred from cells to transform E. coli DH5. The
chromosoroal._ DNA of yeast was prepared according to the
method described in Methods in Yeast Genetics - A
Laboratory Course Manual - Rose, M.D. et al., p. 131 - 132,
Cold Spring Harbor Laboratory Press, NY. Digestion of seven
plasmid DNA (pCARSl, pCARS4, pARS5, pCARS6, pCARS7, pCARSB
and pCARSIO) collected from E. coli with various
restriction enzymes revealed that either of these plasmid
DNA comprises 5 - 7 kb inserts. In addition, when the ATCC
9950 strain was transformed with the plasmid DNA by the
electric pulse method, 6418-resistant transformants were
obtained for either of the plasmid DNA. It was confirmed
from this result that DNA sequences having autonomous
replicability have been cloned in these plasmids. By the
analysis with a variety of restriction enzyme digestions
that pCARS7 and pCARS8 of these plasmids comprise the same
insert. These results indicates that six DNA fragments
having autonomous replicability in the yeast Candida utilis
have been cloned.
Further, a genomic DNA library of the yeast Candida
utilis was prepared with the plasmid pCLHSIO (Figure 15)
2168Q37
87
described in Example 9 as a vector. The yeast Candida
utilis was transformed with the library together with the
library constructed on the plasmid pGKAPH2. However, no
cycloheximide-resistant transformant was obtained. This
indicates that as a feature of the ARS of Candida utilis,
the number of copies of the plasmid containing it is small
per cell, and the transformants cannot be selected when the
ARS is used with a cycloheximide-resistance L41 gene which
requires seve-wal cwp~.ev for ..selecting a transformant.
Example 27: Shortening of the DNA fragments
containing an autonomously replicating sequences (ARS)
Three plasmids ( p~~ARS5.~: pCaRS6 and pCARS7 ) which
have successfully transfc~-med the yeast Candida utilis at
a high frequency among the seven plasmids in which
autonomously replicating DNA sequence have been cloned in
Example 26 were further analyzed in detail.
The frequency of trans'.-'ormation of yeast with these
three plasmids was examined with the BglII-digested DNA of
the chromosome-integrated plasmid pCLRAPHl prepared in
Example 19 as a control. The ATCC 9950 strain was
transformed with 0.1 ug of DNA under the pulse condition of
an electric capacitance of 25 ~aF, a resistance of 1,000 S2
and a voltage of 5 KV/cm. The post-pulse culture was
carried out for 4 hours. The result is shown in Table 7.
Table 7: Frequencies of transformation with a variety of
ARS plasmids
Plasmid Number of colonies
pCARS5 16450
pCARS6 9500
pCARS7 4700
pCLRAPHl 400
Note 1): Number of traps=ormanzs per ~
Note 2): pCLRAPHl was digested with BglII before use.
2~6~~3'~
88
This indicates that the frequency of transformation
which is about 10 - 40 times higher than that of the
integration of DNA with rDNA as a target is obtained with
the plasmids containing the ARS.
In addition, these plasmids pCARS5, pCARS6 and
pCARS7 were digested with Notl and recyclized with T4 DNA
ligase to construct plasmids pCARS50, pCARS60 and pCARS70
from which the 3.3 NotI fragment containing the PGK gene
promoter, the F.rT gene and tile PGK gene terminator was
deleted. The:.~e 'three nevi plasmids were examined on the
length of their inserts with a variety of restriction
enzyme digestion. Thus, all these plasmids had inserts of
about 5 - 6 kb, so that ~:he recd:.,ns having autonomous
replicability was further ,limited. Eacrt of the plasmids
pCARS50, pCARS60 and pCARS70 was partially digested with
Sau3AI to collect 1 - 3.5 kb fragments, which were ligated'
to the plasmid pGKAPH2 which had L~3e~:n digested with BamHI
and dephosphorylated with T4 DN%~ ligase. E. coli DH5 was
transformed with each of the three DNA solutions, and
plasmid DNA mixtures were extracted from 2,500 - 6,000
transformants to prepare DNA libraries. The ATCC 9950
strain was transformed again with 5 ug portions of the DNA
according to the electric pulse method described in Example
11 to obtain 6418-resistant transformants.
The 6418-resistant colonies thus obtained had a
variety of sizes, and five transformants of each of the
three libraries which had formed a relatively large colony
was further cultured in YPD medium containing 200 ug/ml of
6418. Total DNAs were prepared from cells thus obtained,
and E. coli DH5 was transformed with the DNA. No
transformant of _E. coli was obtained with some of the G418-
resistant strains. Moreover, when the ATCC 9950 strain was
transformed again with these plasmids collected according
to the electric pulse method described in Example 11, some
of these plasmids were excluded as they showed an
extensively low frequency of transformation as compared
with the original plasmids pCARSS, pCARS6 and pCARS7.
,~. ",~
89
Finally, a plasmid containing a shortened DNA fragment and
having a transformation frequency similar to that of the
parent plasmid was obtained from each of pCARS50, pCARS60
and pCARS70. The plasmid derived from pCARS50 was referred
to as pCARSS-2, the one derived from pCARS60 as pCARS6-2
and the one derived from pCARS70 as pCARS7-2, respectively.
The restriction enzyme maps of the chromosomal DNA
fragments containing autonomously replicating sequences in
these six plasmids thus obtained are shown. in Figure 38:
Plasmids containing further:shortena._,d DNA fragments
were constructed from the three plasmids pCARSS-2, pCARS6-2
and pCARS7-2 which have the shortened chromosomal DNA
fragments to examine their transformation frequencies . 4~h~:~-.
the partial DNA sequences of some of the plasmids
constructed in this process were determined, the abound 700
by region in the left side of the BglII site in pCARS5 im
Figure 38 showed a homoJ_ogy of 90~ or more to the about r.v0
by reg~oi: in the lE.ft side of the EcoRI site in pCARS~6-2.
This results suggested that the insertion DNA fragments of
pCARS5 and pCARS6 are derived respectively from the
homologous chromosomes or repetitive sequences, though they
have different restriction enzyme maps. Therefore, the
following analysis was conducted on the insertion DNA
fragment of pCARS6 and pCARS7. The autonomously replicating
sequence contained in pCARS6 was referred to as CUARS1, and
the autonomously replicating sequence contained in pCARS7
was referred to as CUARS2, respectively.
Example 28: Shortening of DNA fragments inserted
in pCARS6 and pCARS7 and transformation frequency and
plasmid stability
(1) Shortening of the DNA fragment inserted in
pCARS6 and transformation frequency
The DNA fragment cloned in the plasmid pCARS6-2,
which was partially digested with Sau3AI, had a size of
about 1.9 kb. Thus, three plasmids containing parts of the
inserted fragment of pCARS6-2 were constructed in order to
2.168~3'~
further limit the autonomously replicable region. These
plasmids were constructed by the following procedure.
The 3.3 kb Notl fragment containing the APT gene
expression cassette was removed from pCARS6-2 to construct
5 pCARS6-20. The plasmid pCARS6-20 was digested with AflII
and Xbal, treated with Klenow enzyme to form blunt ends,
and recyclized with T4 DNA ligase to construct a plasmid
pCARS6-210. The plasmid was ligated with a 2.3 kb Notl
fragment containing the APT gene expression cassette~with
10 a shortened PGK gene promoter which~was cut out,.from the
plasmid pGKAPH3 to construct plasmid pCARS6-12. The
plasmid pGKAPH3 was constructed by treating the EcoRI.site
in the promoter fragment of the plasmid pGKAPHl cons :bruited
iii Example 19 with Klenow enzyme to form blunt r-_~rds, to
15 whicY: Notl linkers (5'AGCGGCCGCT3': SEQ ID NO: 18) were
iigate3. Etch of pCARS6-20 and pCARS6-21 was digested W tii
HindIII, recyclized with T4 DNA ligase, and then ligated.
with the ~.3 kb Notl fragment containing the APT gene
expression cassette with the shortened PGK gene promoter in
20 the same manner as above to construct plasmids pCARS6-22
and pCARS6-23, respectively. The restriction enzyme maps of
the insertion DNA fragments contained in these five
plasmids are shown in Figure 39.
The ATCC 9950 strain was transformed with each of
25 the .plasmids thus constructed according to the electric
pulse method described in Example 11 with 1 ug of DNA under
the pulse condition of an electric capacitance of 25 uF, a
resistance of 1,000 n and a voltage of 5 KV/cm. The post
pulse culture was carried out for 4 hours. The result is
30 shown in Table 8.
2~.6803'~
91
Table 8: Transformation frequencies and stabilities of a
variety of plasmids derived from pCARS6
Number of transformants per 1 ug of plasmid DNA
Plasmid Number.of colonies (%)
pCARS6 1093 (100)
pCARS6-2 710 (65)
pCARS6-21 137 (13)
pCARS6-22 253 (23)
pCARS6-23 25 (2)
Note 1: Data express the average values of double
experimental runs.
Stability of plasmid
Plasmid o
pCARS6
21.4
pCARS6-2 31.9
pCARS6-21 29.9
pCARS6-22 11.0
pCARS6-23 3.9
Note: Generation number is between 2.5 - 3.5 generation.
The stability of each plasmid in yeast was examined
according to the following procedure. The 6418-resistant
colonies thus obtained were inoculated in 4 ml of a YPD
medium and cultured with shaking at 30~C for 8 hours. The
cells were spread on YPD plate and a YPD plate containing
6418. Numbers of colonies were compared with each other
after culturing for 2 days for calculating the retention
rate of the plasmid. The results are shown in Table 8. The
absorbance of the culture showed that the cells have
divided 2.5 - 3.5 times. It was also revealed from the
2168~~'~
92
result that of the plasmids pCARS6-21 and pCARS6-22 in
which the insertion DNA fragment of pCARS6-2 had been
shortened from the both sides showed great decrease in
transformation frequency, although the pCARS6-21 showed the
stability similar to that of pCARS6-2. Also, with respect
to the CARS6-23 in which the insertion DNA fragment had
been shortened to 0.6 kb, transformation frequency was
further decreased to 1/50 as compared with the
transformation frequency with pCARS6. These results
indicate that CUARS1 contained in pCARS6 is difficult to be
shortened than the about 1.9 kb DNA fragment of pCARS6-2.
(2) Shortening of pCARS7 insertion DNA fragment
and transformation frequency
The DNA fragment cloned in the plasmid pCARS7-2,
which was partially digested with Sau3AI, had a size of
about 3.5 kb. Thus, in order to further limit the
autonomously replicable region, five plasmids containing
parts of the pCARS7-2 insertion fragment were constructed
according to the following procedure.
From plasmid pCARS7-2, the 3.3 kb NotI fragment
containing the APT gene expression cassette was removed to
construct plasmid pCARS7-20, which was then digested with
Xbal, recyclized with T4 DNA ligase, and ligated to the 2.3
kb NotI fragment containing the APT gene expression
cassette to construct pCARS7-4.
In addition, an about 1.8 kb EcoRV-HindIII
fragment, an about 1.3 kb Xbal-HindIII fragment, and an
about 1.8 kb HindIII-BglII fragment were cut out from
pCARS7-20, and ligated to pBluescriptIISK- (Stratagene)
digested with wither EcoRV and HindIII, XbaI and HindIII,
or HindIII and HamHI, respectively. The 2.3 kb NotI
fragment containing the APT gene expression cassette with
the shortened PGK gene promoter was ligated with the
plasmid to construct pCARS7-6, pCARS7-7, and pCARS7-8. The
restriction enzyme maps of the insertion DNA fragments
contained in these six plasmids are shown in Figure 40.
The ATCC 9950 strain was transformed with each of
....
2~sso~~
93
the plasmids thus constructed according to the electric
pulse method described in Example 11 with 1 ug of DNA under
the pulse condition of an electric capacitance of 25 uF, a
resistance of 1,000 S2 and a voltage of 5 KV/cm. The post-
s pulse culture was carried out for 4 hours. The result is
shown a.n Table 9.
Table 9: Transformation frequencies and stabilities of a
variety of plasmids derived from pCARS7
Number of transformants per 1 ~.g of plasmid DNA
Plasmid Number of colonies
pCARS7 1833 100
pCARS7-2 1273 69
pCARS7-4 U 0
pCARS7-6 598 33
pCARS7-7 *280 15
pCARS7-8 5 0.2
Note 1: Data express the average values of double
experimental runs.
Note 2: * indicates that colonies have very small sizes.
Stability of plasmid
Plasmid %
pCARS7 23.0
pCARS7-2 34.9
pCARS7-6 18.6
pCARS7-7 11.4
pCARS7-8 7.0
Note: Generation number is between 2.5 - 3.5 generation.
The stability of each enzyme in yeast was examined
-.
2~68~3'~
94
according to the following procedure. The 6418-resistant
colonies thus obtained were inoculated in 4 ml of a YPD
medium and cultured with shaking at 30'C for 8 hours. The
cells were spread on YPD plate and YPD plate containing
6418, and numbers of colonies were compared with each other
after culturing for 2 days for calculating the retention
rate of the plasmid (Table 9). The absorbance of the
culture showed that the cells have divided 2 . 5 - 3 . 5 times .
Tr~ese results indicated that the transformation frequencies
with the plasmids pCARS7-2 and pCARS7-6 decreased to about
70 o and about 30% as compared with that of pCARS7 . However,
the stability was not so lowered. UJhile the plasmid pCARS7-
7 containing a further shortened DNA fragment showed the
transformation frequency of 1/2 as compared with pCARS7-6,
it generated colonies very small in size and showed poor
stability (Table 9). On the other hand, transformation
frequency was poor with pCARS7-8, and no transformant was
obtained with pCARS7-4. These results indicate that CUARS2
contained in pCARS7 may be shortened to the 1.8 kb DNA
fragment of pCARS7-6, while the transformation frequency
decreased.
These two results with respect to the shortening of
ARS indicate that a relatively long region is necessary for
the ARS of the yeast Candida utilis to have an autonomous
replicability. This is a very interesting feature, which is
different from the fact that the about 200 by ARS of a
yeast of the genus Saccharomyces shows its function
(Newlon, C.R and Theis, J. Current Opinion in Genetics and
Development, 1993, 3, 752-758).
Example 29: Determination of the DNA sequences of
DNA fragments containing the autonomously replicating
sequence of pCARS6-2 and pCARS7-6 and Southern analysis
(1) Determination of the DNA sequences of DNA
fragments containing autonomously replicating sequences
The DNA sequence of the DNA fragments containing
ARS, CUARS1 and CUARS2, in pCARS6 and pCARS7 were
2.~~8~3'~
determined. Plasmids having a variety of deletion mutations
were prepared by deletion with ExoIII nuclease and mung
bean nuclease from the both ends of the insertion DNA
fragment of pCARS6-2, as a DNA containing the CUARS1 and
5 the insertion DNA fragment of pCARS7-6 as a DNA containing
the CUARS2 in order to determine the DNA sequences . The DNA
sequence of the insertion DNA fragment of pCARS6-2 is shown
in Figures 41 and 42, and the DNA sequence of the insertion
DNA fragment of pCARS7-2 is shown in Figures 43 and 44. The
10 insertion DNA fragment of pCARS6-2 comprises 1921 by and
has a ratio of A + T to the total bases of 69.50, and the
insertion DNA fragment of pCARS7-2 comprises 1788 by and
has a ratio of A + T to the total bases of 70.8-°x. It has
been thus revealed that either of the DNA fragments have a
15 very high ratio of A + T.
Computerized analysis revealed that as compared
with the 11 by sequence (T/A)TTTA(C/T)(A/G)TTT(T/A) T~;hich
are commonly observed in ARS (Newlon, C.R. and Theis, J.,
Current Opinion in Genetics and Development, 1993, 3, 752-
20 758), 9 consensus-like sequences (which are different in
one base from the consensus sequence) are present in
pCARS6-2 and similar 13 consensus-like sequences are
present in pCARS7-6, 5 sequences being overlapped with each
other (Figures 41 - 44).
25 (2) Calculation of number of copies by Southern
analysis
In order to evaluate the number of copies of the
plasmid containing ARS in the cell of the yeast Candida
utilis, Southern analysis was conducted on the DNA prepared
30 from the yeast Candida utilis which had been transformed
with pCARS6 or pCARS7 (Figure 45 -1). In addition, since
the PGK gene was used as an internal standard for
calculating the number of copies, Southern analysis was
conducted for calculating the number of copies of the PGK
35 gene (Figure 45 - 2).
Southern analysis for calculating the number of
copies of the PGK gene was conducted with DNA prepared from
.~. 216~~3~~
96
2 strains of the ATCC 9950 transformed with the plasmid
pCLLACl described in Example 18, which had been digested at
the SphI site in the PGK promoter, and with DNA prepared
from the parent strain as a control. When the 0.4 kb EcoRI-
XbaI fragment containing the PGK promoter cut out from
pGKPT4 described in Example 4 was used as a probe for the
DNA digested with SalI + NotI, a 3.2 kb band derived from
the endogenous PGK gene was observed in the ATCC 9950
strain as the parent strain (Figure 45-2, lane l). On the
other hand, in the strain in which pCLLACl digested with
the Sphl site in the PGK promoter had been integrated, in
addition to this 3.2 kb band, a 5.4 kb band generated by
NotI digestion of plural plasmids integrated in tandem, and
two bands of 6.4 kb and 2.1 kb generated by disrupting one
of the chromosomal PGK genes by the insertion of the
plasmids were detected. (lanes 2 and 3). Since these two
6.4 kb and 2.1 kb bands were generated from the NotI site
in the plasmid molecule and the SalI site in the PGK gene
region at the both sides of the integrated piasmid
molecule, the plasmid molecule was revealed to be
integrated in the PGK gene locus by homologous
recombination.
When the densities of these bands were measured
with an Imaging Analyzer (Fuji Film), the 3.2 kb band
derived from the endogenous PGK gene and the 6.4 kb and 2.1
kb bands derived from the plasmids at the both ends of the
plasmid molecules integrated in the chromosome had almost
the same densities in the transformant. Thus, it was
indicated that there are 2 copies of the PGK gene per cell,
and in the transformants one of the 2 copies was disrupted
by the insertion of the plasmid DNA. Furthermore, it was
revealed by comparing the densities of the 5.4 kb band due
to the tandem integration of the plasmid and the 6.4 kb and
2.1 kb bands, that the integrated plasmid had about 4
copies.
The DNA prepared from ATCC 9950 strains transformed
with pCARS6 and pCARS7 were digested with EcoRV + Notl, and
2~.6~03'~
97
Southern analysis was conducted with the 0.9 kb XbaI-NotI
fragment containing the PGK terminator cut out from pGKPT4
described in Example 4 as a probe. The result is shown in
Figure 45-1. In the parent ATCC 9950 strain, an about 7 kb
band derived from the endogenous PGK gene was observed
(Figure 45-1, lane 3). In the transformant, a 3.3 kb band
derived from the plasmid in addition to the about 7 kb band
was observed. By comparing the densities of the 7 kb and
the 3.3 kb bands, it was calculated on the assumption that
the 7 kb band corresponds to 2 copies of the PGK gene and
that copy number of pCARS6 and pCARS7 were 1 (lane 4) and
0.4 (lane 2), respectively. Due to the falling out of the
plasmid molecule during cell culture, the number of copies
of pCARS7 might be less than 1. It was considered from the
result that -che plasmid containing CUARS had about 1 copy
per cell.
(3) Existence mode of ARS on chromosome
Southern analysis was conducted on a variety of
chromosomal DNA of the HindIII-digested ATCC 9950, 9226,
9256 and KP-2059 strains and Saccharomyces cerevisiae S288C
strain. With probes: as CUARS1 the 1.3 kb fragment
obtained by digesting pCARS6-22 with Xbal and HindIII
(Figure 39); and as CUARS2 the 1.8 kb EcoRV-HindIII
fragment of pCARS7-6 (Figure 40), hybridization was
conducted (Figure 46). With respect to CUARS1, in addition
to a main 2 kb band which was expected from the restriction
enzyme map of pCARS6, a 1.6 kb band which had the same
length as the HindIII fragment expected from the
restriction enzyme map of pCARS5,was observed (Figure 46-
1). Further, with respect to CUARS2, in addition to a main
2.5 kb band which was expected from the restriction enzyme
map of pCARS7, DNA sequences having a high homology were
present in about 10 copies on the chromosome of the yeast
Candida utilis and also in many copies on the Saccharomyces
yeast (Figure 46-2). It is suggested from the result that
CUARS2 may be an extensively preserved sequence. In
addition, with a severer washing condition (0.1 x SSC,
216803'
98
65~C ) , any signals other than the main one were scarcely
observed (Figure 46-2).
Furthermore, in order to examine whether these ARS
sequences are derived from chromosomal DNA or not, Southern
analysis was conducted on the chromosomal DNA of Candida
utilis separated by the pulse field gel electrophoresis
method. The DNA of the ATCC 9950 strain was separated in
seven bands, in which CUARS1 was located at the 6th
chromosome from the top and CUARS2 was located at the 3rd
chromosome from the top. It was also revealed that the
cloned ARS sequences were derived from chromosome. The
insertion DNA fragment of pCARSS was located at the 6th
chromosome like CUARS1. As indicated from the sequence
analysis described in Example 27, these results supported
the possibility that ARS cloned in these pCARSS and pCARS6
be derived from the homologous chromosomes.
Example 30: Cloning of DNA fragments having
promoter activity with use of ARS
(1) Construction of promoter cloning vector
DNA containing an autonomously replicable sequence
was cut out as a 1.9 kb SacI-Smal fragment from the plasmid
pCARS6-20 constructed in Example 28. The fragment was
ligated with the plasmid pAPHl (Example 19), which was
digested with EcoRI and treated with Klenow enzyme to form
blunt ends, and further digested with Sacl to construct a
plasmid pPCVl. Further, pPCVl was digested with BamHI,
treated with Klenow enzyme to form blunt ends, and HpaI
linkers (5'GTTAAC3') were ligated to construct a plasmid
pPCV2 (Figure 47).
(2) Construction of a library and cloning of DNA
fragments having promoter activity
Chromosomal DNA of the Candida utilis ATCC 9950
strain was partially digested with restriction enzymes
RsaI, HaeIII and AluI at the same time. Then, the DNA
fragments were subjected to electrophoresis with 1% of
agarose gel, and the 0.9 - 1.8 kb long fragments were
99
collected. The partially digested DNA fragments and the
plasmid pPCV2 digested with HpaI and dephosphorylated were
ligated with T4 DNA ligase. E. coli DH5 was transformed
with the DNA solution, and a plasmid DNA mixture was
extracted from about 100, 000 transformants thus obtained to
prepare a genomic DNA library. The ATCC 9950 strain was
transformed with the DNA prepared from this library with
the electric pulse method under the pulse condition of
electric capacitance of 25 uF, resistance of 1,000 S2, and
voltage of 5 KV/cm. DNA was used in an amount of 20 - 25 ug
per pulse. Transformants were selected on a YPD plate
containing 200 ug/ml 6418. Repetitive runs of
transformation gave 380 transfarmants in total with 280 ug
of DNA. Among these transformants, 84 strains in which
relatively large colonies were formed were grown on YPD
plate containing 1 mg/ml 6418. Twelve strains which showed
good growth were cultured in YPD medium containing 1 mq/ml
6418, and total DNA was prepared from the cells to
transform _E. coli DH5.
It has been revealed by the restriction enzyme
digestion that all of the twelve plasmid DNA recovered from
_E. coli, i.e., pPCVl, 3, 9, 14, 19, 33, 51, 55, 57, 62, 64
and 78, contain 0.9 - 1.8 kb insertion DNA fragments.
Further, DNA fragments containing sequences having promoter
activity were cut out with XbaI, and ligated to
pBluescriptIISK- (Stratagene) to construct plasmids.
partial DNA sequences of the plasmids were determined
starting from the both sides of the insertion DNA
fragments. It was revealed from the result that pPCV33 and
pPCV78, or pPCVl4, pPCV51 and pPCV55 have the same DNA
fragment. Therefore, nine DNA fragments having promoter
activity were finally cloned.
When the ATCC 9950 strain was transformed with nine
plasmids pPCVl, 3, 9, 14, 19, 33, 57, 62 and 64 by the
electric pulse method, 6,000 - 10,000 6418-resistant
colonies were obtained per lug of DNA for either of the
plasmid DNA. Moreover, 20 clones comprising 2 strains of 10
216803'
100
6418-resistant strains obtained with the 9 plasmids and
pCARS6-2 used as a control were cultured in 5 ml of YPD
medium overnight, and then separated into single colonies
on YPD plate. Ten colonies of each of the twenty clones
were cultured on a YPD plate containing 6418 to evaluate
the retention rate of the plasmids. As a result, while
pCARS6-2 had a plasmid retention rate of 5%, all of the
other plasmids had an increased retention rate. Among these
plasmids, particularly pPCVl, pPCVl9 and pPCV64 had a high
retention ratA in the range of 80 - 85~. It was thus
indicated that the DNA fragment containing a sequence which
had a promoter activity thus obtained had a function of
increasing the stability of_- the plasmid.
(3) Determination of the DNA sequence of a DNA
fragment having a promoter activity
With respect to the insertion DNA fragment of the
plasmid pPCVl9 among the nine DNA fragments having promoter
activity thus obtained. plasmids having a variety of
deletion mutations were prepared by deletion with use of
ExoIII nuclease and mung bean nuclease to determine the DNA
sequence from the both sides of the insertion DNA fragment.
The determined DNA sequence of the 1054 by insertion DNA
fragment of pPCVl9 are shown in Figure 48.
Example 31: Construction of a plasmid for
expressing hygromycin B-resistance gene and selection of
co-transformants of yeast with use of it
(1) Construction of a plasmid for expressing
hygromycin B-resistance gene and confirmation of its
function
Hygromycin B phosphotransferase (HPT) gene was
obtained by PCR with 2 primers prepared according to the
already described DNA sequence of the HPT gene (Gritz, L.
and Davis, J., Gene, 25, 179-188 (1983)) using the plasmid
pBIB-HYG (Becker, D., Nucl. Acids Res., 18, 203 (1990)) as
a template. As the primers, the DNA sequences:
2I~~~~'~
101
5'-GGTCTAGATATGAAAAAGCCTGAAC-3' (SEQ ID NO: 33) and
5'-GGAGATCTATTCCTTTGCCCTCGGA-3' (SEQ ID N0:34)
were used. The synthesis was conducted to have the XbaI
site which was located immediately in front of the
initiation codon at the 5' side and the BglII site which
was located immediately after the 3' end termination codon.
The HPT gene fragment synthesized was digested with XbaI
and BglII, inserted between the sites XbaI and BamHI of the
expression vector pPGKPT4 (Figure 4) described in Example
4 to construct a plasmid pGKHPTl (Figure 49). The 3.3 kb
Notl fragment containing the PGK gene prompter, the HPT
gene, and the PGK gene terminator was cut out from the
pGKHPTl. The plasmid pAHGl was constructed by insertin5~ the
Notl fragment at the Notl site of the plasmid pF~Cnln
1~ described in Example 30. In order to confirm whether the
constructed HPT gene expression cassette functions or not,
the ATCC 9950 strain was transformed with plasmid pAHGl by
the electric pulse method described in Example 11.
Transformants selected with resistance to 6418 grew in a
YPD liquid medium containing 200, 400 and 800 ug/ml of
hygromycin B, while wild strain used as a control did not
grow in any media and showed resistance to hygromycin B.
After the plasmid pGKHPTl was divided into a
fragment containing the PGK gene promoter, the HPT gene and
the PGK gene terminator, and a vector fragment by digestion
with Notl, they were used for the transformation of the
ATCC 9950 strain. Transformation was conducted by the
electric pulse method described in Example 11, and
transformants were selected on a YPD plate containing 800
ug/ml of hygromycin B. As a result, 168 hygromycin B-
resistant colonies were obtained per 1 ug DNA. This is
almost the same as the transformation frequency with the
NotI digested plasmid pGKAPHl used as a control, 156
colonies per 1 ug DNA. Thus, this result indicates that the
hygromycin B-resistance gene can be used in the direct
selection of transformants of Candida utilis just like the
2~ 68Q3~
102
6418-resistance gene.
(2) Co-transformation of yeast
0.1 ug of the plasmid pPCV64 containing ARS
obtained in Example 30 and 1 ug or 10 ~.~g of the plasmid
pPGKHPTl divided by Notl digestion into the fragment
containing the PGK gene promoter, the HPT gene, and the PGK
gene terminator and the vector fragment by Notl digestion
were mixed, and used for the transformation of the ATCC
9950 strain by the electric pulse method described in
Example 11.
Pulse was applied at the condition of an electric
capacitance of 25 uF, a resistance of 600, 800 or 1,000 S2,
and voltage of 3.75 or 5 KV/cm, with 6 pulse conditions for
the 2 DNA mixtures. Transformants were selected on a YPD
plate containing 200 ug/ml 6418, and about 2,00C - 7,000 of
transformants were obtained under each condition with 0.1
ug of pPCV64 DNA. 500 - 2,000 6418-resistant colonies
obtained under each condition was replica cultured on a YPD
plate containing 800 ug/ml of hygromycin B. The ratio of
colonies showing resistance to hygromycin B to those
showing resistance to 6418 does not vary largely between
the pulse conditions and remains in the range of about 1 -
2%. Further, the 6418-resistant and hygromycin B-resistant
strains were cultured in YPD liquid medium overnight to
obtain strains which became 6418-sensitive by falling out
of pPCV64 which was present as a plasmid. When 40 strains
were examined, 10 6418-sensitive and hygromycin B-resistant
strains were obtained. It was expected in these strains
that the fragment containing the PGK gene promoter, the HPT
gene and the PGK gene terminator was retained on
chromosome. The chromosomal DNA was prepared from these 10
strains, and it was examined by PCR whether the HPT gene
expression cassette was integrated in the chromosome or
not.
As a primer therefor,
primer 1; 5'CAAGTTGATCCTTCTCCGGA3' (SEQ ID NO: 35)
2~68Q3'~
103
which was synthesized on the basis of the DNA sequence
outside 5' end of the PGK gene promoter fragment used for
the HPT gene expression,
primer 2; 5'GAAACTTCTCGACAGACGTC3' (SEQ ID NO: 36)
which was synthesized on the basis of the sequence inside
the HPT gene, and
primer 3; 5'CATCGGGTAAGGTCTACATG3' (SEQ ID NO: 37)
which was synthesized on the basis of the sequence in the
PGK g~.ne terminator fragment used for the HPTgene
expressicr_~were used.
PCR was conducted 30 cycles under the condition of
95~C for 1 minu te; 55'C for 1 minute, and 72eC for 5
minutes. The result were as shown in Figure 50. Figure
50(1) illustrators the electrophoresis of the PCR reaction
products with primer 1 and primer 3. A 2.7 kb amplification
fragmer_t due to the endogenous PGK gene was observed in
every sample, and a 2.6 kb fragment was observed in five
samples of Nos. 3, 5, 7, 9 and 10. Tree 2.2 kb fragment was
considered due to replacement of one of the two endogenous
PGK genes by the fragment containing the PGK gene promoter,
the HPT gene, and the PGK gene terminator used for
transformation. Moreover, the result of PCR of the same
DNA sample with primer 1 and primer 2 is shown in Figure 50
(2). A 1.4 kb amplification fragment was observed for five
samples in which a 2.6 kb fragment was observed, and in
these five clones the endogenous PGK gene was replaced by
the HPT gene by homologous recombination.
2168~~~1
104
Sequence List
SEQ ID NO: 1
Length: 8so
Type: Nucleic acid
Strandedness: Double strand
Topology: Linear
Molecule type: Genomic DNA
Source
Mi~oorganism: Candida utilis
Strain: ATCC9950
Sequence
CTGCAAGCTA c'TTTGTAATT AAACAAATAA CGGGATTATA TGTCAATATC 60
ATTATGATTA
TTTAGGAP.%~A CATf:'~!'~.ACC TTACCCGATG CACCTCCACC AACAAGCCAA120
TTCTGGGTGG
GATGGAACx~'t'T A~'ACACTGCT CGTACGTTGG TCACCAGTGG GTTfGACAAA180
TGTGCCAGCT
GATGACCATC TC:C~TCGTAG ACGTCAAAGT ACTTGTTCAT AT'I'GGCAATG 240
ACAAACTTTT
CTTTATCCGG GGTATATTGC TGCCACCTZG CCTTCAAAAT GGATACCCAT CTTCCCGTTT300
GACAGTTGTG TrTGATACGA. TGACTTGGGG '_T'C'~AApTCACC TTCAATAGCG360
AAGAG
GTTTAG'IGCT GATG'I'C',.C'I'CA CCAAGATTGA AGATGTTAAC TGTGTCATCG420
TAACCGTTAC
AAACAAGGTC ACCAGATCTA TTCCAATCCA CGATGGAAAC TGACAATCTT GAATCATAGA480
CGCCAACAGT GTGAAGAGTC TCCAGGTTAT CATCCCATTC ATCCCAATCA CACGTAGTTA540
CTGTTCTTAG ATCCCAAACC TTCAAAGTTC GATCCAATGA GGCAGTAGCA ATCTGGTTCT600
TATTCATCGG ATTGGTAGTG AATCCACCAA TCTTTTTATT CGACAATCTC AAAACTTGTC660
TTCTTGAGTG ATCGCCTGCT CTTAGGTCAA TTCTGCTGAA TTGTCCTTGC ATTGTTGTGT720
AGTACATTTC ATTGTCGTTG TTGTAATTTA TGTCAGTGAT ACCGACGTCA AAGTCGTTGA780
TGAATAACTG TGAGGACTTC ATGGAGCGTA GATCAATTGA GCGARTGGAC CCATCATACG840
ATGCACTGTA GACCTTCGTC GTGTCATTCA TGTTGAATTC
SEQ ID NO: 2
Length: 1346
Type: Nucleic acid
Strandedness: Double strand
Topology: Linear
Nblecule type: C~enomic DNA
Feature of sequence
Feature key: TATA signal
Location: 1184..1190
Identification method: S
,..,~
21~~OJ'~
105
Source
Microorganism: Candida utilis
Strain: ATCC9950
Sequence
AAGCTTTTGT CTTZTAGGAG CCTTCTTTTC ACCCTGGCTTTCTTCAGACT CCACGCCTCT60
CGCCCGTTTG 'I'TGTTGATCT TCTTCTGTTG CT'1'CTTCGTGAGCTTACCAG TATCCAGATG120
CGTTGTCAGG GCAAGAGGGZ' CATGTTCAAG CTTTCACTTTCAGTC CAATACGTTT180
CCAGGCAGGG ATGTGTTCGC TCATCG~TC.C AGACTCGAGTGGTGAAAACT ATGGCAACCT240
CTACTTCCTT TCCAAACACA CACCGIGCTT ~1GTAG'I'GTGTGCCTAAr'.~AGC TGAATTTTTT3OO
TTCCTTCCAT GCTC~CGCTGC GA'I'GAGCTC.'T AGCCTCGGAG GCTAGCGACG360
GCC('_GCC:'.GC
TATAAAAAAG GCCTGTGAAA ATTTTATCCT CCTCCTTAACGACCCTTCTT TCTCTTCTTC420
ACAT'I'CAAAA ACTTCAAGCA GCTGTCTCTG TTCCTTTC~CTGTGTTCTACC ATTGGATATT480
CCCATTCCCC GTGGAGAACC GAACTGGAGT CTAGCAGCATGCGAGA'I'f'.~AA 540
TATTACACGG
TTTGAGTCTG ATACGCTTGA GCAGCCATTT TTTGGCTTCTCCTGGTGTGT ATCCAGATAT600
AGAAGTTCGT ATACATTTCC CATAGCGATT GTAAAATGATTCTGCAATGG AACCATCCGT660
AATTGTAGGC CTGCTGAGAT GGCACTCGCA ATGCCTCTGTGTCTGGTT2~'T TTGCCTTCTC720
C'.GTC'CATCAG CACCAGTGGC TTCTTAGGGC GGCTCCTTGG 'T_'GAAAGATGC780
ATAACGAGAC
CCTGCTCCGT CTGTCTGCCT GTTGCTACAA CCACTGCGTAGTCAGATG~C CCGGTCTGTG84C
TGCTGTGGAA TCACCC~GAG CGAAATTCCG GT'1'TCGCTGGCAGATGAGCT CATCAACCAC900
ATCAACTGGA GCAACCTCAC CAGAGGACAC GTAACCTGCCCGGTTGAATT C'I'GTCAAACC960
GTACATCACA CAACAACAGC AGCAGCAACA ACAACAACGTCAGTTGTCGT TCGCATGGCG1020
ACGTTACCTA ACGGCACCAA CATCGTCTCG TCCTCGCCAATGCCTGTTTC CCCTACCCGG1080
AGTGGCCCGG CCCACCTGTC GTTCTTTTTT CGTCAATTGTGTCCAGCTGG TGCCATCACC1140
ATATGTTCAA GTGCGTGGCC TGTACTAGCG CAGTCTGCTGCAGTATAAAA GGGATTGCTG1200
AGGOCCCCTT TAGCGTTTCC AATTAACAAT TGATTCCCTTTTCCCCATAG TCCGTTTGTA1260
CTACATCCTA CATAAC:AAAA GTGAGTGTTA CAAGACAAGTGTGGCGGTCA ATTGGATCAT1320
TTGGACTAAC ATACTGGCGG ATAAAG
SEQ ID NO: 3
Length: 2330 bases
Type: Nucleic acid
Strandedr~ess: Double strandNucleic acid
Molecule type: Genomic DNA
Feature of sequence
Feature key: CDS
Location: 1259..2059
2168~3'~
106
Source
Micxnorganism: Candida utilis
Strain: ATCC9950
Seques~oe
AAGCTTATGG AGGAGATTGG GAAGATTGAA CGAGGTGAGA TGGACACGTT 60
GCTGATTGAC
GAGATCGGCA AGAAGGAGGC ACC'I'GTGGTG AAACCACTTA CACCCGACGT 120
GGATAGTAAT
GTAACAGGGG AACCGACTGG ACATAGTTCT ACGACACCAC CACCGGTGGA 180
ACAGGACTCG
AGCACAACCA CGAGGAAGAG AGCACAAGAC GA'I'GGTGAGG AAAACACAAG 240
GAAGAAGCCC
AAGGTTGAGG CAGAGAAA?',~. GGCAGAGCAA GAGGCAGAGA AAGAGGCAGA 300
GAAAGAGGCA
GAGAAAGAGG CAGAGCi~PI"=A GGCAGAGAAA GAGGCTCCGC G'IGC:AGTGCC360
GAACAAGAGA
CTACAACACA 'I'1'GCZ'ACTCC TCTCATCGAG AGCATCTCGT CATACAAGTA420
CGCCTCAGCG
TTTCTACACC CTGTTAACGA GTCCAGTGCA CCCAACTATT ACTCTCTGAT 4$0
CAAGAAACCA
AGGGATCTGA AGACCATCAA ACAGATGGTC AAGGACGGAC GTATACAGAC 540
CAATCTTGAG
C'I~GAGAGGG AGATCT'IGCT GATGTTTGCC 11ATGCl,',p,TCA TGTACAACAA600
GACCGGGACG
GATATCTACG AGTGGACCAA GGAGATGCAG CCGGAAGTTG ACAAGCTCAT 660
CGAGCTGTTT
AACGAGAGTA AATAGGATAC AGGCTAGAGA TCAAAAGAAG AATAGAAACA 720
GCTCGATAAA
ACGGTATTGT AAGTGGTATG TACAAAGGGG TGZGTCTTC''C: TCAACGTCTT 780
TGCAM'CTG'CT
3AGTCAAAGC AGCGTTCTGC TCTTGGAATC TAAGAC~.:GAC TCTTTCCGAA 840
TGCTTGAGGA
ACTTTTCAGA GCACTTCAAC ACACAGGATT CCTCCTTTGA TGATAGCTTT 900
TCAGAGGTGA
AGTCGTTGAC ACAGTCGCTG AAACAACGCT CAACGAGGTT GGAATAAAGA 960
CGCATAAAGT
CCTTCATCTG CTTCTGCTCA ACAAGCTGCT GGAACTGCTG CTGCTCTTTT 1020
GGGTTCAATT
GGTCCATCCT TGCTACTTTT CCGCCTAGTT TCGATTCCGA TTCTGATAGA 1080
GAAGCCCAGC
TATGAATGGA AGAAATTTTT CACTI~'GTA TGTCCTTTTT TTCACGCTTC 1140
GTTGCTTCGG
ACAAAAAAAT AGTGGAGGCA CTCGGTGGAG GGAAGCTATC CTCGAGATGA 1200
AAAATTTCAA
GCTCATCTCA TCGTCCAAGT GGGACAGCAA GCTGAGGCTT CTGAAGAGGT 1258
TGAGGAAA
ATG GTC ACC ACG TTA TCG TAC ACA GAG AGG GCA TCG CAG CAC 1306
CCT TCG
Met Val Thr Thr Leu Ser Tyr Thr Glu Arg Ala Ser Gln His
Pro Ser
1 5 10 15
CCA CTT GCT AAG CGT CTG TTT TCG CTT ATG GAG TCC AAG AAG 1354
ACG AAC
Pro Leu Ala Lys Arg Leu Phe Ser Leu Met Glu Ser Lys Lys
Thr Asn
20 25 30
CTG TGT GCC AGT GTC GAT GTT CGT ACC ACA GAG GAG TTG CTC 1402
AAG CTC
Leu Cys Ala Ser Val Asp Val Arg Thr Thr Glu Glu Leu Leu
Lys Leu
35 40 45
GTT GAT ACG CTT GGT CCT TAT ATC TGT CTG TTG AAG ACG CAT 1450
ATT GAT
Val Asp Thr Leu Gly Pro Tyr Ile Cys Leu Leu Lys Thr His
Ile Asp
50 55 60
216803'
107
ATC ATT GAT GAC TTC TCT ATG GAG TCT ACT GTG GCT CCA CTG TTG GAG 1498
Ile Ile Asp Asp Phe Ser Met Glu Sex Thr Val Ala Pro Leu Leu Glu
65 70 75 80
CTT TCA AAG AAG CAC AAT 'I"I'C CTC ATC TTT GAG GAC CGT AAG TTT GCT 1548
Leu Ser Lys Lys His Asn Phe Leu Ile Phe Glu Asp Arg Lys Phe Ala
85 90 95
GAT ATC GGC AAC ACC GTC AAG GCA CAG TAC GCC GGT GGT GCG TTC AAG 1594
Asp 11e Gly Asn Thr Val Lys Ala Gln Tyr Ala Gly Gly Ala Phe Lys
100 105 110
ATT GCG CAA TGG GCA GAT ATC ACC AAC GCC CAC GGT GTC ACC GGT GCA :L642.
Ile Ala Gln Trp Ala Asp Ile Thr Asn Ala His Gly Val Thr Gly Ala
115 120 125
GG'~ ~ ATC G'I'C ~ AAG GGG TTG AAG GAG GCT GCA CAG GAA ACC ACG GAT GAG 1690
G:!.y I7_e Val Lys Gly Leu Lys Glu Ala Ala Gln Glu Thr Thr Asp Glu
130 135 140 145
CCA AGA GGG 'i:~ ~ '1'TG ATG CTT GCG GAG CTG AGC TCC AAG GGC TCC TTG 1738
Pro Arg Gly Leu Leu Met Leu Ala Glu Leu Ser Ser Lys Gly Ser Leu
150 155 160
GCC CAC C~G ACA TAT ACC GAG GAG ACC GTG GAG ATT GCC AAA ACT GAT 1786
Ala His Gly Thr Tyr Thr Glu Glu Thr Val Glu Ile Ala Lys Thr Asp
165 170 175
AAG GAC TTT TGT ATT GGA TTC ATC GCA CAG AGA GAC ATG GGT GGC AGA 1834
Lys Asp Phe Cys Ile Gly Phe Ile Ala Gln Arg Asp Met Gly Gly Arg
180 185 190
GAA GAT GGG TTC GAC TGG ATC ATC ATG ACA CCA GGC GTG GGA CTC GAC 1882
Glu Asp Gly Phe Asp Trp Ile Ile Met Thr Pro Gly Val Gly Leu Asp
195 200 205
GAT AAG GGC GAC TCC CTG GGC CAA CAG TAC AGA ACT GTC GAT GAG GTT 1930
Asp Lys Gly Asp Ser Leu Gly Gln Gln Tyr Arg Thr Val Asp Glu Val
210 215 220 225
GTC AGT GGT GGC TCT GAC ATC ATC ATC GTT GGT AGA GGC TTG TTT GGA 1978
Val Ser Gly Gly Ser Asp Ile Ile Ile Val Gly Arg Gly Leu Phe Gly
230 235 240
AAG GGA AGA GAT CCA ACA GTG GAA GGT GAG CGT TAT AGA AAA GCA GGC 2026
Lys Gly Arg Asp Pro Thr Val Glu Gly Glu Arg Tyr Arg Lys Ala Gly
245 250 255
216037
108
TGG GAT GCT TAT CTC AAG AGA TGC TCA GCT CAA 2059
Trp Asp Ala Tyr Leu Lys Arg Cys Ser Ala Gln
260 265
T AAGCGTTGAG CTCTGGCTTG TATAGGTTCA CTTGTATAAA 2100
ATGTTCATTA CTG'I'I'hI'CGG AAGITGTAGA TTGCCATTTT TGCGCAAATT GACGCCAGTC 2160
TTTTTTTGCG CCAAATGTCA GTTTTTTTGC GCCAAAATTT ACTTCATCTT ATACAACTGC 2220
AAAAACCATC CAA'I'CCAATC CAGAAAGGAC TGATCAATGG TGGTGATTGA CTCAAGTTCT 2280
GATGCTACAC AACAGACAGA GCTCTCTAAA AAGAATTCGA TATCAAGCTT
SEQ ID NO: 4
Length: 258 amino
acids
Type: amino acid
u9olecule type: peptide .
Sour:..:~e
Microorganism: Candida
utilis
Strain: ATCC9950
Sec~uenr~
Met Val Thr Thx~ Leu Tyr ThrGlu Ala Ser HisPro Ser
Ser Arg Gln
1 5 10 15
Pro Leu Ala Lys Arg Phe SerLeu Glu Ser LysThr Asn
Leu Met Lys
20 25 30
Leu Cys Ala Ser Val Val ArgThr Glu Glu LeuLys Leu
Asp Thr Leu
35 40 45
Val Asp Thr Leu Gly Tyr IleCps Leu Lys HisIle Asp
Pro Leu Thr
50 55 60
Ile Ile Asp Asp Phe Met GluSer Val Ala LeuLeu Glu
Ser Thr Pro
65 70 75 80
Leu Ser Lys Lys His Phe LeuIle Glu Asp LysPhe Ala
Asn Phe Arg
85 90 95
Asp Ile Gly Asn Thr Lys AlaGln Ala Gly AlaPhe Lys
Val Tyr Gly
100 105 110
Ile Ala Gln Txp Ala Ile ThrAsn His Gly ThrGly Ala
Asp Ala Val
115 120 125
Gly Ile Val Lys Gly Lys GluAla Gln Glu ThrAsp Glu
Leu Ala Thr
130 135 140 145
Pro Arg Gly Leu Leu Leu AlaGlu Ser Ser GlySer Leu
Met Leu Lys
150 155 160
2168037
109
AlaHisGly Tyr ThrGlu Glu Thr Val Ile LysThr
Thr Glu Ala Asp
165 170 175
LysAspPhe Ile GlyPhe Ile Ala Gln Asp GlyGly
Cys Arg Met Arg
180 185 190
GluAspGly Asp TrpIle Ile Met Thr Gly GlyLeu
Phe Pro Val Asp
195 200 205
AspLysGly Ser LeuGly Gln Gln Tyr Thr AspGlu
Asp Arg Val Val
210 215 ~ 220 225
ValSerGly Ser AspIle Ile Ile Val Arg LeuPhe
Gly Gly Gly Gly
230 . 235 240
LysGlyArg Pro ThrVal Glu Gly Glu Tyr LysAla
Asp Arg Arg Gly
245 250 255
Trp Asp Ala Tyr Leu Lys Arg ~ys Ser n.ra Gln
260 ?55
SEQ ID NO: 5
Length: 2086 bases
Type: Nucleic acid
Strandedness: Double strand
Molecule type: Genomic DNA
Feature of sequence
Feature key: intron
Location: 1115..1481
Identification Method: S
Feature key: CDS
Location: 1111..1114
1482..1795
Source
M_icroorgarusTn: Candida utilis
Strain: ATCC9950
Sequence
GGATCCAATC GT'I'GAAAGTG ATCAAGCTGA TTACAAAAGT AAGTATGAAA AGAGCCAATG 60
TTGAGAGTCT CAGGAACCAC ATCGACTTCT TCGTGCCATC CTCCCACATT CTGAAGCCCA 120
AGAACCCACA AATCATCAAA CACCAACACG ATGCGGACGC CAACCCGAGT TGTAACGCCA 180
CAAAGTACGG GTACGACCCT GTTCCAGGAG GGCTCACGCC GCAATCAACA ACCAAAGTCG 240
CCACGATCAA CGCCAGTATC AAGTAAAAGA AGAATAGCAT CTCCAGTCTT CCGATAGCTG 300
,....
2168~3'~
110
TGTACTTCGA TCTGACGTTG TAGATGATGA 360
TGATCATGAT CACGAGGGCA CCAATGTTGA
CAAAGGCGTT ACCAATCTGG AATATCACGGTATTGGCAAC GTCTA'I'CGGA CGGGCGTAGC420
ACTCAGGGAT GATCCCTTCG TTCAGGTGCGTGAACTGCTC GTTCGTCGTT GCCTTCACAA480
CC'IY~GCACAA CGGGAGCGGC GTGTTGTGGCATAGCGAGTT GAAATCACCG AATGCCATTG540
TGTTTZ'ATCG TTAGGGAC'~AC CTGTTTGAAGCTGACAGCGG GATGAAGATG AGGAAGGAGA600
GCACAACAGC TGAGCGGAAG TCTCTGTGATGCTTGGTGGA CCC,GGTGTAG GTGGAATCTC660
CCTGGTGAGC GTACTTGCAA CGGTGCTCAGCGACTTCTTC TCGAGAGGAA ACGTAAACAA720
AGAGGTTTCA ATGTTGATGT TGATGTGTATTTTTGTTACA AAAGCAGAAA TTGTAAACAA780
AAAGGTATAA TTAGGGCTCT GGTGTAATGATGGGCACGTG ACGTTACCGT GCTGGTCGAT840
TTTAGGGCTA TTGGTTCGC:G TCCCGCTGGTGTCCGGGTTA GCGZ'GTCAAT GTGGCGCCTC900
CCGATTATTA CATAAGAAAA CACCCACCCACGCAACACCT GGTGTCTGGA TGTTGACGCT960
TTGTATGCGT GTGTGTGTTT TTTCTTCCGTCTTGTTGCGC CACTC'T'GCGC GAGCGTTGGC1020
GACTCACCGG TGAAATTTAT CGAAAACTTTCAGGCTCAGG CCCTTTTCAA CACTACCCTT1080
TGAGATCACA TCAAGCAGTA ATCAAACACA 1110
ATG G GTATGT GGGAAACGAC 1130
Met Val
1
GACGrGTGCG GTGTGTGAAT GCCATTAGTG GGATATGTGG TAGTCTCGAG CGTGGATATT 1190
ATCGATAGGG ATGGTGCTTG TTCTATACGT CTTGCTGGGA AGGAAGAAAG CGATGAAGTA 1250
TGTGGGAAGA AGGGGTGGTZ' TAAGAGAGGA AGTAGACATG TAACAAGTGT GTTCAGAGAA 1310
CAAGGACGGA AATATCACCT ATATGACGTA CACATCACGA ACTGCTCCTG GAGGAAGCGA 1370
CAAGATGAAT ATCAACAGGC ATCATCATAT CTCTACAATG GCTCGT'I'CCC AAAGCACACG 1430
CACAAACAAA TCCGAGACTT TTGTACTAAC AGCTGTATCT CTGACAAATA GTT AAC 1486
Asn
GTTCCA AAG AGA AGA TAC TGTAAG GGTAAG TGC AGAAAG 1534
ACC ACC GAG
ValPro Lys Arg Arg Tyr CysLys GlyLys Cys ArgLys
Thr Thr Glu
10 15
CACACT CAA AAG GTT CAG TACAAG GCTGGT GCT TCCCTC 1582
CAC ACC AAG
HisThr Gln Lys Val Gln TyrLys AlaGly Ala SerLeu
His Thr Lys
20 25 30 35
TTTGCC CAG AAG CGT TAT GACCGT AAGCAA GGT TACGGT 1630
GGT CGT TCC
PheAla Gln Lys Arg Tyr AspArg LysGln Gly TyrGly
Gly Arg Ser
40 45 50
GGTCAA ACC CCA GTT CAC AAAAAG GCTAAA ACC AAGAAG 1678
AAG TTC ACC
GlyGln Thr Pro Val His LysLys AlaLys Thr LysLys
Lys Phe Thr
55 60 65
d
2~0303~
111
GTT GTT TTG CGT TTG GAG TGT GTT GTC ACC AAG GCC CAA TTG 1726
TGC AAG
Val Val Leu Arg Leu Glu Cys Val Val Thr Lys Ala Gln Leu
Cys Lys
70 75 80
GCT TTG AAG CGT TGT AAG CAC TTC GAG GGT GAC AAG AAG CAA 1774
TTG GGT
Ala Leu Lys Arg Cys Lys His Phe Glu Gly Asp Lys Lys Gln
Leu Gly
85 90 95
AAG GGT CAA GCT TTG CAA TTC TAAGCTTAAGACAATTGTTGAAAGT TTTATTATTA1830
Lys Gly Gln Ala Leu Gln Phe
100 105
TCACTACACT G~!'GTWA TGTCATCTAA TGTAAAAGCGTTTATATTAC CACTTGGTTC1890
GGTATCCTGT AGAAGAATAC GGCCTGTAGC GTAGCATTCCCACAGGAGGA TCACAGCAAC1950
ATAGACCAAA CAATGTCACG CACGGGGATC GAACGCGGAACCAAACCTCT CCCTCCTCCC2010
CCTTTCACCG CGGTTATTTT GTTATGGGCA CACACAGGGGAAGGAAAAAA ATGCACACAC2070
GCACAAAAGC GAGCTC
SEQ ID NO: 6
Length: 106 amino acids
Type: Amino acid
Molecule type: Peptide
Source
Microorganism: Candida utilis
Strain: ATCC9950
Sequence
Met Val Asn Val Lys Thr Arg Tyr Cys Gly Lys
Pro Arg Thr Lys Glu
10 15
Cys Arg Lys His Gln His Val Gln Tyr Ala Gly
Thr Lys Thr Lys Lys
20 25 30
Ala Ser Leu Phe Gln Gly Arg Tyr Asp Lys Gln
Ala Lys Arg Arg Ser
35 40 45
Gly Tyr Gly Gly Gln Thr Lys Pro Val Phe His Lys Lys Ala Lys Thr
50 55 60
Thr Lys Lys Val Val Leu Arg Leu Glu Cys Val Val Cys Lys Thr Lys
65 70 75 80
Ala Gln Leu Ala Leu Lys Arg Cys Lys His Phe Glu Leu Gly Gly Asp
85 90 95
216803'
112
Lys Lys Gln Lys Gly Gln Ala Leu Gln Phe
100 105
SEQ ID NO: 7
Length: 975 bases
Type: Nucleic acid
Strandedness: Double strand
Molecule type: Ger~anic DNA
Source
Micxoorqaniszn: Candida utilis
Strain: ATCC9950
Sequence
AAGCTTACAGCGAGCACTCA AATCTGCCCT CCGAGCCCTC CGGCCCTCTC TTCAACAAAC60
TCGCGCTGCACTTCGTCGrC AG'rGG'1'GCCA ATCACCCAAC GTGGAGGTAT 120
CAAGAGGTGC
TCCAGCCCACAAAGCGACAT CAAAGACAAC AACCCTGCCG GCCTACGTCC TACACACCCT180
GGTGATCGCAGACATTGTAC AAGGTGC',CAC GCAATAACCT ACAGGCACCG 240
CACATGACGA
TGGCCTTGGTTGTGCAACCA GTGi-~CTTCCA CGGTCCACGC AGCAACATGA 300
ACCACACCAC
CCAGAATCGATGCGCGCAAC AACAGTTGTT CCGGTTCACT CAGCCCCACA GCGAGTCGCT360
GGCAGAACACGAGCCTGAGG GCGGAAAGAG GGTAGAGGAA AGCGCAAGGA CAGGGGACAA420
CCTGGCCCAATTGATGTCAT ATAAACCCTC TCGATCAATT GAGCACACTC ATCCGCCAAT480
TGACCCCTGTTCC~CAGCTCC ACGC',CCCATG TTCCTCGTCC CTGGTGTAGC 540
TTCTCCCCTA
AATTCCAGCGCTTGGTTCCG CCCTCCCTGT CTCCCGGGTT TAACGAACGT GTGTACCATC600
TGATGGTAATCCGCTCCCGT CCGCGCF1ACA CAACTCACAA GCAGATCACA CCTGTACACG660
CCGCTGCTGATGCGCCCAAT TTAATTTTTT TTCTCTCAAT GTAGGGGAGA AGCCTTGGGA720
GCTCCCGACTCCCAGTTGGG CACAGCTGCC ACCTCATGAC TTTTCCTGTG TGTGCCTGTC780
TGACGTTACGTGTGATGTAG TGGCCCCCGT TCGGTGTGTT TTCGCCTGTT GCGCTGTGCC840
CCCCTTAAAAGTATAAAAGG AAGTGCAATT GCTGTTTGTG TTGATTGTTG ATCCTTGTTT900
CCTCTGTTTCCTCCTCATCA CACAAGAAAG GTTTCTTCTT TCCAACAGAT ACAAAACACA960
CTTACAAACAACATA
SEQ ID NO: 8
Length: 802 bases
Type: Nucleic acid
Strandedness: Double strand
Molecule type: Genomic DNA
Source
Microorganism: Candida utilis
2168~3'~
113
Strain: ATCC9950
Sequence
ATTGTATGAC TTTTATTTAT GGGATTACGT TATAAATTAT GATCCTCATGGATTATCTTA60
TTAAGrCTCC ATCZ"rGTAGC TTGTAATATG ATGAACACTC CAGGTAATTC120
GTGAGTTTTC
ACCGTGCCTC GTCCATGCAC TTTTATCAGC CTCGACGTCA TACATTGCATGGTGAGTAAC180
TGGAAAACGG CTTTTTACGT TCTGTTGTAT ATGGCTAAAC GCTTCTATGGCACGGCGCTA240
TTAACCI'GTC TGACATTTCA ACCTGGTGTT GATGGCTTAA GGTGAGATAT300
ACGATAATAC
ATAGCTAACA GAAT GACGCACTGA TTCCACTGTA TATATAGGCGATATGTGTTG360
TTGGATGGAC GTTTCTTTGT CTCCTGATCC ACAATAGTAG CTCAGCTCCGTGCCAACTGG420
TrCGCTGGTA CGATAGTGAG GGATGAATGA AACCTTTTCG TTTTCTTCTGCGCTTCCACG480
GAAC'~TA GATTTCTCTC GTGAATAGCG AGTTAAGCCA CGAGTGGGGTCTGCAATTGA540
AGG'I~GATA CCAGAGTCAA AAGTTZGGAT GTGATGGAAA CTTCAAAGGCTTCTCGGTGG600
TATATCAAAC GATTCACAGA GGTAGAAGCG GATCTTGAAG GCCAGAATATGCATTAAAAC660
CAGCGTATAT CAGTTTTGCT TTCCCAGAGA GGACTTTTGC ATTATTCTTCAGCTTTATCC720
CTGGATTTTG GGAGATGAAA CATTGACAAA GCTGGT'I'CGT ACTTGCCTAC780
GATCCTAAAT
TGACTCCTGA GGTATTACAC GT
SEQ ID NO: 9
Length: 599 bases
Type: Nucleic acid
Strandedness: Double strand
Molecule type: Genomic DNA
Source
Microorganism: Candida utilis
Strain: ATCC9950
Sequence
TCTAGAGCTG TCGACGCGGC CGCGGAATTA ACCCTCACTA AAGGGAACGA 60
ATTCGGATCG
GTGTTTTGGG CAGTGGGACC AAATCGATGC CCATGTTGTT TTTTTGTATT 120
TTCGCAACTT
TTTCCCCATT CGGTCATACC GAAGGCGGTT CAAGCCTGCA AGAGACAACA 180
ACTATGGCTG
CTGTTCTTGG AATGAAAATA AACGCATTTG GAAGTTTTGC AGCCAAAACA 240
GGATGCGTTT
TCGCCATTTC GG'IGCGGCAT TTCCGGTTTC AGATTTTCGC GAAATTTGTT 300
TT'I~CCATCA
AATCTC-~CAAA TTT<:GGAAAC GGGCCGCGCT GATTGGCTGC GTCCTGAAGC 360
C~GCAATTTTT
CTCCC'I~TCG TTTGTTGATA CAACCAAGAA TTTCTTTTCG TGCTCTGCGC 420
CAGCGCTATC
CAAATGTTTA TAAATCTTGA TGTGATTTCC CGTTTTCTGT CCTTGCTCAT 480
TCTGTCTCTC
TGTTGAACCA TTGTTGTTTT ACGAACTCAA GGTCCAATTG GAACAGTATG 540
TGCACTGCCA
ATGGAGCATT GAAAGGGTTA TTCGATGTCG TCACCACGTG ATACTAACCA
TTGATATAG
114
SEQ ID NO: 10
L~erlg-th: 1188 bases
Type: Nucleic acid
Strandedness: Double strand
Molecule type : C~er~m.ic DNA
Source
Microorganism: Candida utilis
Strain: ATCC9950
Sequen~oe
GCCGCTAATA CCCCTTAGGT TI"ICGZ'TTCA TACATAGAGT GGTTGTTGTT 60
TAACATTTTA
TCGTGATTAA TTTTTAATCG AGTAATATAT TATTGGAAAA GTTTTTAGAC 120
TTTGAAGCGT
AGTATCGGTG GCTT'I'GCGGA GCTTAGCGCT GTGTCCTTTC TCCGTTGTTT 180
ATGGAGTGTT
GATGTTTTGT GATTTACAGC GATGTCCGGG TTT'ITGTGTA CACGCTC-~C".CC240
TTGAACCAAA
AAAAAAGCTG CTGGGAATCG ATCGAGGGAA AAAACATCAC CAAAAAAAAA 300
ACAAACAGCA
GAAAGTAAAC AAACAACATT ACAAACAACA ACATCACACA GCGGCACGCT 360
TTAAACCAGG
GCGGTAGTGA CGTGAG"I'rGC TTGTTTTCGA TCAGCGAGTG CGGTGTTA'1'C420
GATATCZ1'CG
AATCTGCTTA TAGTTCAAGA ACGC'~'GGAT CCCAAGCGTA G"I'GAAGTGTT480
CrCTTTTGTT
TACTTI~TGT TTTGTATATT AGT'I~GGAAC CCATTAGAAA AGGTTCATCT 540
CTGAGATAAA
GAGCAAAGAC GCACGAGACA ATCAATCATT TGAGATGGGA TCAGTATCAG 600
CGGAGAGTGC
TGATAAGATT GAGGAGAACA GAGCAACTGG GGCTTGTTTG GACATTCTCT 660
CACCACCAAA
GCCTTCGTCA ACGTCCACAC CACCTACAGC GACTGCTGCT GCCATTGGCG 720
GGTCTGGTAA
TGAAACCAGT GACAGCTTCA ATCCTTTTGA GAAGGACTCA CTGGATGAAT 780
CTGCTTCGGT
GTTATCCACA AAGCAACTGC TTGCTGAGGG ACAGGGATCA AATGCCCTGC 840
CATCTGAACT
CGTTGATATC AACTTGC~JGA TTAGCGCTCT TAACTTGGAC TTTGACGGTC 900
AAAAACGTGG
ACAAACTACA GCCAC'rACAG AGCCAGTAGG TGTTTTGAAA GATGGTGCCG 960
AACCTAGTGC
TACAGGATCA GACGACCACC CGCCACCAGC TCTGTATCCA CCAGGTATGA 1020
TCCCACAGCA
CATGCCATTT TTCCCGCTAA ACGAATTTGG ACAGCCAATG CATGCACCAT 1080
TCCCTGGAGA
CCATCCACAT AGTCCAATCC CGTGGGATTC CAAACCTGGA CAGACTCCTT 1140
TTGGTTTAAT
GGGATCTCAT GGCCCAAATA TGGATGGGTT ACGCTCACAA ATGGTACC
SEQ ID NO: 11
Length: 1921 bases
Type: Nucleic acid
Strandedness: Double strand
Molecule type: Gen~nic DNA
Source
Microorganism: Candida utilis
216~03'~
115
Strain: ATCC9950
Sequence
GATCATGrTT CGTACAAAAC ACCGCCACTC CGTTATGAGA AAGTCATAGT 60
TATATTTCGG
GGAAACTTAT GTTGCTrGCA AGGAATAATA GACAGACAAA TGTTTTACGA 120
AACTGAAGGA
TTAATACAAT TGATGCAAAA AAACAAAAAA AAAAAAAAAA AAAAAAAAAA 180
AAAAAAAACA
AAAACACAAA AACACAAAGA AAAAAAACAC AAAGAAAAAA AACACAGAAC 240
ATCCAAAACA
AAACAACAAT ATATATATAT TTGCTAATAC CATCACCCTC CCTCATACAA 300
AAAAAAAAAG
AAAA'I~GAAG GAGCACGTAT ATCTTTTCTA TGATCTTTGG ATATGGAATA 360
GATAAGCAAC
CCCTCTAGTG AAGTACACAT CAAGATACTT GGGGAGCAAA CTGAGAGCAC 420
ATGATATACA
CGAAAGCCAC CATATATCAT ATATAAAAAT ATGAAACATG AAAAGTTATT 480
CATCTGTTGG
ATTCACTTTT ATATGTTTTC ATGCATTGTC TACTCTATGC CTCTGTCTTT 540
TCTCTGTTCC
TTTACACTCC TCTATTATCA AATTGAGTGT TTCATTTATC AAAGAAGTTT 600
GAGCTGGATC
AGAACTTTAG ATATTt.'ATTC CTGTTTrCGA TATATCTATA CGATGTTCTA 660
ATATCCACTC
TCACTACCAT TGTTAAAAAA AGTTAAAATT ATAGCTGTGT GCCTTAAGGG 720
AATAAAGGAA
ATGGATCTTT TGAATGTTAA AAAACGAGAT ACTCTTTTGT AAACCAGAAA 780
ACGAT'I'TTCA
AAACACAAAT TGGTGAATGT CACCAAGCAA AAATTGTATC CTAAAAAAAA 840
TAAATTTATG
AACTAAATTA TCTCTGAAi.A GACATTTAGT CAACCTTTTC TCCTTGCTCC 900
TCGGTCAAAG
GTTTTTCGrA TAGATATATA TACGGGTTGC TTTTTTGTTT CCACTCGTCT 960
AATCGAGTTT
CGATATCAAT GGAGATTTAT TCTTTGGCTT TGATTCCATA ATAATCCATA 1020
TCCTAATAAA
ACACTTTGAA GCGAATrGAA ACCCCAATAT CTTTCTGGCC ATTAAAACAT 1080
TTATAAAGTA
CTGGATGTTT AAAGAGCTTZ' GAGAATrGCC TAGCT~CAAA ATATATTTGT 1140
CTCCAATTAT
GATTTZGTAT TTTCCZT'1'CT TTGTTTTCTG TAGTTATTTA AAATAAGTTC 1200
ACTACGTTGT
TTTTTGAGGA ACCGTTACTC TATTTACTCA AATTTATTAT CAAAATGTTT 1260
TTTTTTCGTT
TGATTTATTC AAATGCTGTC GATATGTCCC AGAAATATCA TACAATTCAA 1320
ATTTCTAAAG
CCAGCGTTTA TTATAAAGCT TTGAGTTCTT TCGACTTAAT TACATGTATG 1380
TAGCTCAAAC
CAAAGTTACT CTATAATTAT AAAAAGACTA TGAACCAATT CAAGAATTCC 1440
CCATTTCCAG
CAAATTTAGT ATAGCTCAAA TTCACACTGT CATATGCAAA AACCTAAATA 1500
AGCAGATCAT
TGTAAAGAGC CGGCAGTTGT ATATTCCAGT GGGCCTGAAC TTG"I'GGTTAG 1560
GATTCACAGA
CATCTTGTTG TCGGATrTCT ATTGATAGAA GC'I'GTGCCAT TGAAAATGGA 1620
AATATAAAAT
GGTATTGGGT TGATCATATA TGAATTTCTT ATTACTCATA ATAATAGGAG 1680
AAATCATCGA
ACATGGAACA TAGATGCTAA TTAAGGTACG TACAGCATCC TGTTCAATAT 1740
TTCAACTTTT
TAAGTATTAA ATTAGTGAAG AAATGTATTA TGAACCATTG TTCAATAATT 1800
CTAATGTG"I'T
TTTTGTGGTT TTTTTTTTGG CTTTTGGGAC ATTGTAATTT TTACTCATTT 1860
ATTCGATGTC
TCTTCAGGTT TTTGTGTTTT TTTTTTTTGT GTTTAAATCT TCGCGGAATT 1920
GAGATAAGAT
C 1921
216$Q3~
116
SEQ ID NO: 12
Length: 1798 bases
Type: Nucleic acid
Strandedr~ess : Double strand
Molecule type: Gen~nic DNA
Source
Microorganism: Candida utilis
Strain: ATCC9950
Sequence
AAGCTTATAG AATTTGAAGA TATAAAAACA CAACAAAGCT ATGAAAGC:AA TGAGGG("'~ACG60
ATTTGATGAA CAGAAGGAGC TATTCCCATT AATTTAATAT CTACCAATAG ATATGTCAGT 120
CAAACATGTC AGAAGTCATA CTCACTAATT ATATGAGCGG GTGCGTTAGA TATTTATATG 180
P,GT'I"I~"-f'.ATC TTTCTACATG GGGCTTTCAA GTAACTGGAA GTAATACAAC TTTTGTTTAA2:~0
GTTGATAAAA ACAAAAAACA AAAAAACAAA AAACAAAAAA ACAAAAATAA AAAAAAAAAA 300
AAACAAAAAA AAAAAAACAC ACACGCACAC ACACACATAT ACAAACACAT ACAAAAAACT 360
TA'i'CA'1'aATT AAGATAAATG AAAGCTATCT AAAATTTCCA GACATTTTCT GAAAAAGTGG420
CTGCI'..F:GCTT TATTGCTTTG CTTTAAATTT ATAAAGAAAA CTTCZ"rTGAA ATCGAATATG480
AAF~CAAGAGG AAACGGATGA AAGGATAAAA CACAAATACA GGAAAACATT ATTACAAATA 540
AAGCACCTGZ" AAGAGATAAA TTTGTTACAT TTAAAGGATT CTACTTACAT ATACAGAGAA 600
AGCAATrTCA TAGACATAGG GTCTACCGAA CAGTCTTGAT ATTTCAGACT AGTATTTTTG 660
TTGTATTATG GGGCTTGGTC GGTATGTTAG TAAAAAGTTC ATTTTAAAAT TTTCCAAGAA 720
GTGTZTTTAT TGCAGAAAAA TATCCGTGGT TCAAGAGATA ATGGGCTGTA AATTTGTTTT 780
GTACCAAAAA TATCTTAATT AATACAAAGA ATACCTTTTA TGAAGGTAGA TCAAGATCTT 840
AAATTTCATT ACTCAGAAAT GAATATACTT GAAACTTCCG AAATACTATG TTATGGGGAA 900
CAAATAAGAG GAGCCATTTC ATATTTATTT TGGAAAGATC GTTTTCTATG CGCAGTTGTT 960
GGAATAGCGA TATTATCATG ACCTTATATT CAGTCAGAGA AAATAGGGTA CGAATTTGAA 1020
AACAA'I~TTT CAGCTTCAAA GAGGACCTTT AAACGGTCAG GCAAAAGTTG AGGTGTCAGT 1080
GTGTATAAAA ATGTTCAATT CATTTTTGGT TGAAAGATGC TTTAAAAGGT TGGTGCAAAG 1140
AATCATATAT GTGTATTGGC TAGTTAAAAG TTGCTTTATT AAAAATATAT GCAAACTAAA 1200
TTGTCTATAC GATTGATAAG GTGAAACTTA GATAAACAAT GAAAAAGGAA GGTGCTTTGA 1260
AAACCGACCA GCTTCAAATA AATATGTAAC TATTTTTATG GATGTGAAAA TTAAATGTTG 1320
TCGAATCTGC TGTTTCTAGA TTTGTAGATG AAAATGTTGA CGTGAGAGTT TTCATTTGTT 1380
TGTATTTTAT ATTATGG"rTT GATTACTACT CATAGCTTGG GTTTAGCATG GCCTGAGTAA 1440
GTAGGAAGAT CCAATAAATT GACTGTTGTC GTTTTGAAAT TAAATACTGA AATGAATAAA 1500
AGTTTGACGA GAAAAGACCT GAAATATATA AAAATGTTTT GTATTATTTA AGTCGGTTAC 1560
ATTCTCTCAC TTTATTGTAA CAACCATTAT AGTGATGGGG AAAAAATAAA ACATAAGCCA 1620
CATAAGGAGA TATTGTTCTT TATTGAAAGG ATGGAATCAT TTTCTGGAAA TGTCAP~AAAT 1680
k
2168Q3'~
117
TAAATATTAC TTGGTTTTTG ATGAATTGTA GAAGAAAAAG TAAATGCTGC TAT'I~.'TC'I'TT 1740
CTTTACATTT TCCACTGATTCTGG CTATGTGACT TTAAGTTGTT GAGATATC 1798
SEQ ID NO: 13
Length: 1054 bases
Type: Nucleic acid
Strandedness: Double strand
Molecule type: Gerwcnic DNA
Source
Micxnorganis~n: C~dida utilis
Strain: ATCC9950
Sequence
CCACATITGT TGTACGAGAA GGGCC'.AACGA CAGCTCTCTT 'hI'GGAGATAA60
CGAGGAAGAC
GCCTTGCTTG ATTTGTAATC TTCAAGAGAG AGCTC'I'TTGT GTTGAGTGTC120
AGCTTGTCTT
TGAGAAGCAT TTGTGCAATG AATATGGGAG AGATGAGATG AGTAGAGAGCAGCACAAGTG180
GAATCAAATC ACAATAACAA CTTTAGCCAC AGGGAGGTTA AAAGAGGAGAAGAAGGAGTC240
CTTTCCAATT GTfCGCTAGTG CAGAAGAGAA AATTTC~TTG GGTGTGTATG300
CTACAATCGT
CAAACCCGTT GTAAAGGTGG TGTCTTTGTA TATGTAGGG"r GTCTCGAGAA360
GTGTGGCTTC
AGCACATAAG CTGTGGCGCA CTTTC:TCGGG TAAGTGATTT GATCTCAATT420
AATTGCACGT
TCT'I~T~TTG AAGCCACTAA AGCTTACGTA AGCGACCACG TGGGAZGTTT480
GATCTGGTGT
TGGTTTTGGG AGGGGCAGGG GGTTTACATG TZGGCTTTAT CGATTGCGGCGCTTTGTGTT540
TGGGGGTGTA TGCCCTAGCG ACCCTGTGGG CCACTGCCCA GGTGCCCAGGTGCGACCAGG600
AAAAAAATTT CTZ'CATCGCT AGAGCTTTCT TCAACCCCCT ATTCTTTTCA660
TTCTTTCCTA
ACTAACAACA AATAAACACA GTAACAAGAT GTCATCTGAC CTTTCAGACGTTAGACTCTT720
TGTCAGACCA CTI'CCATTCG ATGTTAACGA AGAGGACTTG TCTCCCCTAT780
AAGAGCTTCT
TGGTGAAATC ACCGATTTCA TCGTTGCTAG AGGTTATGCC TTTGTTGAATACGCTAATGC840
AGATTTC~CA AGACAAGCCA TCGCTGAATT GCACCAAAAG CCGTTCGGTGATGTTCCATT900
ATCCTTGGAG TACGCTAAGG C'I~AAAAGCC AAGATTCAGA CTAACATGCC960
CTTCTTGTTT
AGAAGGTGCT GAGZGGCAAG A'I'C'lGAAAGA TTTTGCTCTC TCGAAGTTAC1020
CAAAAGGGAT
CTACGCCAAC GTTTTCCAAA GAGAGAACAA CGGT
SEQ ID NO: 14
Length: 30 bases
Type: Nucleic acid
Strandedr~ess: Single strand
Molecule type: Synthetic DNA
Feature of sequence
2168Q37
11$
Feature key: primer
Sequence
GGTCGACATA TCGTGGTAAG CGCC~I'TGTCA 30
SEQ ID NO: 15
L~erigth: 30 bases
Type: Nucleic acid
Strandedr~ess: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Sequence
TTCTAGACTT TATCCGCCAG TAZ'G'ITAGTC_' 30
SEQ ID NO: 16
Length: 33 bases
Type: Nucleic acid
Strandedness: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Sequen~oe
GGGTACCTAA CTGCAAGCTA CTTTGTAATT AAC 33
SEQ ID NO: 17
Length: 30 bases
Type: Nucleic acid
Strandedness: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Sequer~ce
GGAATTCAAC ATGAATGACA CGACGAAGGT 30
SEQ ID NO: 1$
Lrer~gth: 10 bases
Type: Nucleic acid
21~8~3'~
119
Strandedness: Double strand
Molecule type: Other nucleic acid
Sequence
AGCGGCCGCT 10
SEQ ID NO: 19
Length: 30 bases
Type: Nucleic acid
Strandedness: Single strand
Nblecule type: Synthetic DNA
Feature of sequence
Feature key: primer
~~quenoe
ACCACTATTA CCACTACGGT TTGCTCTACA 30
SEQ ID NO: 20
Length: 30 bases
Type: Nucleic acid
Strandedness: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Sequence
GACACATCTC TGAGCAGCAT GACTTGGTTG 30
SEQ ID NO: 21
Length : 12 bases
Type: Nucleic acid
Strandedness: Single strand
Molecule type: Synthetic DNA
Sequence
CTAGATGGTA GG 12
SEQ ID NO: 22
Length: 10 bases
Type: Nucleic acid
2168~3'~
120
Strandedness: Double strand
Molecule type: Ott~x nucleic acid
Sequence
SEQ ID N0: 23
L~erig-th: 31 bases
Type: Nucleic acid
Strandedr~ess: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Sequence
CCAAGCTTAC AGCGAGCACT CAAATC'I'GCC C 31
SEQ ID NO: 24
L~er~gth: 36 bases
T~-pe: Nucleic acid
Strandedr~ess: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Sequence
CCTCTAGATA TGTTGTTT~"I' AAGTGTGTTT TGTATC 36
SEQ ID NO: 25
Length: 30 bases
Type: Nucleic acid
Strandedness: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Sequer~e
GGGATCCATT GTATGACTTT TATTTATGGG 30
SEQ ID NO: 26
Length: 30 bases
121
Type: Nucleic acid
Strandedr~ess: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Sequence
GGACTAGTGA GATGACTCTA GGCATCTTCT 30
SEQ ID NO: 27
L~eng-th: 26 bases
Type: Nucleic acid
Strandedness: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Sequence
ATGACTGATA CATCATCCTC TTCATC 26
SEQ ID NO: 28
I~~gth: 28 bases
Type: Nucleic acid
Strandedness: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Sequence
TAACGACAGC 'I'GGCAAACCG ACTGGGAC 28
SEQ ID NO: 29
Length: 34 bases
Type: Nucleic acid
Strandedr~ess: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Sequence
GGCGGCCGCA ATTAACCCrC ACTAAAGGGA ACGA 34
2~ 68037
122
SEQ ID NO: 30
Length: 32 bases
Type: Nucleic acid
Strandedr~ess: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Sequence
TTCTAGACTA TATCAATGGT TAGTATCACG TG 32
SEQ ID NO: 31
Length: 25 bases
Type: Nucleic acid
Strandedr~ess: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature. key: primer
Sequence
CCGGTACCTA AGCCGCTAAT ACCCC 25
SEQ ID NO:
32
Length: 35
bases
Type: Nucleicacid
Strandedness:Single strand
Molecule type:Synthetic DNA
Feature of ence
sequ
Feature key: primer
Sequence
GGGCGGCCGC ACTCGCTGAT CGAAA 25
SEQ ID NO: 33
Length: 25 bases
Type: Nucleic acid
Strandedness: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
2~ ~8~3~'
123
Sequer~e
GGTCTAGATA TGAAAAAGCC TGAAC 25
SEQ ID NO: 34
Length: 25 bases
Type: Nucleic acid
Strandedness: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Seque~~ce
GGAGATCTAT TCCTTTGCCC TCG~'aA 25
SEQ ID NO: 35
Length: 20 bases
Type: Nucleic acid
Strandedness: Single strand
Nblecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Sequence
CAAGTTGATC CTTCTCCGGA 20
SEQ ID NO: 36
Length: 20 bases
Type: Nucleic acid
Strandedness: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Sequence
GAAACTTCTC GACAGACGTC 20
SEQ ID NO: 37
Length: 20 bases
Type: Nucleic acid
2I6~03'~
124
Strandedness: Single strand
Molecule type: Synthetic DNA
Feature of sequence
Feature key: primer
Sequence
CA'I~GGGTAA GGTCTACATG 20
